bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel small molecule that induces cytotoxicity in lung cancer cells inhibits disulfide reductases GSR and TXNRD1
Authors: Johnson Fraser D. , Ferrarone John , Liu Alvin , Brandstädter Christina , Munuganti Ravi , Farnsworth Dylan , Lu Daniel , Luu Jennifer , Sihota Tianna , Jansen Sophie , Nagelberg Amy , Shi Rocky , Forcina Giovanni C. , Zhang Xu , Cheng Grace S. W. , Spencer Miko Sandra E. , de Rappard-Yuswack Georgia , Sorensen Poul H. , Dixon Scott J. , Guha Udayan , Becker Katja , Djaballah Hakim , Somwar Romel , Varmus Harold , Morin Gregg B. , Lockwood William W. 
Published: June 2021

AbstractHigh-throughput phenotype-based screening of large libraries of novel compounds without known targets can identify small molecules that elicit a desired cellular response, but additional approaches are required to find and characterize their targets and mechanisms of action. Here we show that a compound termed lung cancer screen 3 (LCS3), previously selected for its ability to impair the growth of human lung adenocarcinoma (LUAD) cell lines, but not normal lung cells, induces oxidative stress and activates the NRF2 signaling pathway by generating reactive oxygen species (ROS) in sensitive LUAD cell lines. To identify the target that mediates this effect, we applied thermal proteome profiling (TPP) and uncovered the disulfide reductases GSR and TXNRD1 as LCS3 targets. Through enzymatic assays using purified protein, we confirmed that LCS3 inhibits disulfide reductase activity through a reversible, uncompetitive mechanism. Further, we demonstrate that LCS3-sensitive LUAD cells are correspondingly sensitive to the synergistic inhibition of glutathione and thioredoxin pathways. Lastly, a genome-wide CRISPR knockout screen identified the loss of NQO1 as a mechanism of LCS3 resistance. This work highlights the ability of TPP to uncover targets of small molecules identified by high-throughput screens and demonstrates the potential utility of inhibiting disulfide reductases as a therapeutic strategy for LUAD.
Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1
Authors: Okada Hajime , Saga Yumiko 
Published: June 2021

AbstractOrganisms are inherently equipped with buffering systems against genetic perturbations. Upregulation of homologous genes responding to gene loss, termed genetic compensation, is one such buffering mechanism. Recently, a well-conserved compensatory mechanism was proposed: transcriptional adaptation of homologs under the nonsense-mediated mRNA decay pathways. However, this model cannot explain the onset of all compensatory events. We report a novel genetic compensation mechanism operating over the Mesp gene locus. Mesp1 and Mesp2 are homologs located adjacently in the genome. Mesp2 loss is partially rescued by Mesp1 upregulation in the presomitic mesoderm (PSM). Using a cultured PSM induction system, we reproduced the compensatory response in vitro and found that the Mesp2-enhancer is required to promote Mesp1. We revealed that the Mesp2-enhancer directly interacts with the Mesp1 promoter, thereby upregulating Mesp1 expression upon the loss of Mesp2. Of note, this interaction is established by genomic arrangement upon PSM development independently of Mesp2 disruption. We propose that the repurposing of this established enhancer-promoter communication is the mechanism underlying this compensatory response for the upregulation of the adjacent homolog.
DAB2IP inhibits p53 ubiquitin-mediated degradation by competitively binding to GRP75 and suppresses tumor malignancy in colon cancer
Authors: Shen Jie , Feng Shengjie , Deng Jiao , Huang Qingwen , Zhao Dayong , Jia Weiyi , Li Xiaolan , Tao Deding , Gong Jianping , Xie Daxing , Liu Liang 
Published: June 2021

AbstractIncreasing evidence has shown that DAB2IP acts as a tumor suppressor and plays an inhibition role in many tumors. However, the underlying mechanism is still uncertain. Our study shows that DAB2IP is positively associated with a better prognosis in colon cancer patients with wild-type TP53 expression. In vitro assay shows that DAB2IP elicits potent tumor-suppressive effects on inhibiting cell invasiveness, colony formation and promoting cell apoptosis in wild-type TP53 colon cancer cell lines. Subsequently, DAB2IP is demonstrated to up-regulate the stability of wild-type TP53 by inhibiting its degradation in a ubiquitin-proteasome-dependent manner. Using mass spectrometry profiling, we unveil that DAB2IP and p53 could both interact with the ubiquitin ligase-related protein, GRP75. Mechanistically, DAB2IP could competitively bind with GRP75, thus reducing GRP75-mediated p53 ubiquitination and degradation. Finally, animal experiments also reveal that DAB2IP inhibits the tumor progression in vivo. In conclusion, our study presents a novel function of DAB2IP in GRP75-driven wild-type p53 degradation, which provides a new insight in DAB2IP-induced tumor suppression and provides a novel molecular aspect of the p53 pathway.
Nanoscopical analysis reveals an orderly arrangement of the presynaptic scaffold protein Bassoon at the Golgi-apparatus
Authors: Ghelani Tina , Montenegro-Venegas Carolina , Fejtova Anna , Dresbach Thomas 
Published: June 2021

1.AbstractBassoon is a large, 440 kDa, scaffold protein of the specialized sites mediating neurotransmitter release from presynaptic nerve terminals, called active zones. At active zones of the brain, Bassoon is arranged with its C-terminus facing the plasma membrane. In young, cultured neurons Bassoon is associated with the Golgi-apparatus, where it may assemble active zone precursors structures, but whether or not Bassoon is an extended protein at the Golgi-apparatus and whether it is arranged in an orderly fashion is unknown. Understanding the topology of this large scaffold protein is important for models of active zone biogenesis.Here, we generated recombinant Bassoon constructs for expression in neurons, with tags positioned to allow for the specific detection of N- and C-terminal regions of Bassoon by single-domain antibodies, called nanobodies. Using stimulated emission depletion (STED) nanoscopy in cultured hippocampal neurons, we confirmed that recombinant Bassoon is oriented with its C-terminus towards the active zone plasma membrane at synapses. Focusing on the soma, we found that an intramolecular tag located immediately downstream of amino acid 97 of Bassoon, showed prominent colocalization with markers of the trans Golgi network, including TGN38 and syntaxin-6. In contrast, tags located immediately downstream of the C-terminal amino acid 3938 of Bassoon showed significantly less colocalization with these Golgi-markers. The intramolecular N-terminal tag was located between 48 and 69 nm away from TGN38, while C-terminal tags were located between 100 and 115 nm away from TGN38. Sequences within the first 95 amino acids of Bassoon, but not its N-myristoylation sequence, were required for this arrangement.Our results indicate that at the Golgi-apparatus Bassoon is oriented with its N-terminus towards and its C-terminus away from the trans Golgi network membrane. Moreover, they suggest that Bassoon is an extended molecule at the trans Golgi network with the distance between amino acids 97 and 3938 estimated to be between 46 and 52 nm. Our data are consistent with a model, in which the N-terminus of Bassoon binds to the membranes of the trans-Golgi network, while the C-terminus associates with active zone components, thus reflecting the topographic arrangement characteristic of synapses also at the Golgi-apparatus.
Sleep spindle frequency: overnight dynamics, afternoon nap effects, and possible circadian modulation
Authors: Bódizs Róbert , Horváth Csenge G. , Szalárdy Orsolya , Ujma Péter P. , Simor Péter , Gombos Ferenc , Kovács Ilona , Genzel Lisa , Dresler Martin 
Published: June 2021

AbstractHomeostatic and circadian processes play a pivotal role in determining sleep structure, timing and quality. In sharp contrast with the wide accessibility of the EEG index of sleep homeostasis, an electrophysological measure of the circadian modulation of sleep is still non-available. Evidence suggests that sleep spindle frequencies decelerate during biological night. In order to test the feasibility of measuring this marker in common polysomnographic protocols, the Budapest-Munich database of sleep records (N = 251 healthy subjects, 122 females, age range: 4–69 years), as well as an afternoon nap sleep record database (N = 112 healthy subjects, 30 females, age range: 18–30 years) were analysed by the Individual Adjustment Method of sleep spindle analysis. Slow and fast sleep spindle frequencies were characterized by U-shaped overnight dynamics, with highest values in the first and the fourth-to-fifth sleep cycle and the lowest values in the middle of the sleeping period (cycles 2–3). Age-related attenuation of sleep spindle deceleration was evident. Estimated phases of the nadirs in sleep spindle frequencies were advanced in children as compared to other age groups. Additionally, nap sleep spindles were faster than night sleep spindles (0.57 and 0.39 Hz difference for slow and fast types, respectively). The fine frequency resolution analysis of sleep spindles is a feasible method of measuring the assumed circadian modulation of sleep. Moreover, age-related attenuation of circadian sleep modulation might be measurable by assessing the overnight dynamics in sleep spindle frequency. Phase of the minimal sleep spindle frequency is a putative biomarker of chronotype.
Inhibition of Casein Kinase 2 induces cell death in chronic myelogenous leukemia cells resistant to tyrosine kinase inhibitors
Authors: Mitrovský Ondřej , Myslivcová Denisa , Macháčková-Lopotová Tereza , Obr Adam , Čermáková Kamila , Ransdorfová Šárka , Březinová Jana , Klamová Hana , Žáčková Markéta 
Published: June 2021

AbstractChronic myelogenous leukemia (CML) is a myeloproliferative disease characterized by the presence of a BCR-ABL oncogene. Despite the high performance of treatment with tyrosine kinase inhibitors (TKI), about 30 % of patients develop resistance to the therapy. To improve the outcomes, identification of new targets of treatment is needed. Here, we explored the Casein Kinase 2 (CK2) as a potential target for CML therapy. Previously, we detected increased phosphorylation of HSP90β Serine 226 in patients non-responding to TKIs imatinib and dasatinib. This site is known to be phosphorylated by CK2, which was also linked to CML resistance to imatinib. In the present work, we established six novel imatinib- and dasatinib-resistant CML cell lines, all of which had increased CK2 activation. A CK2 inhibitor, CX-4945, induced cell death of CML cells in both parental and resistant cell lines. In some cases, CK2 inhibition also potentiated the effects of TKI on the cell metabolic activity. No effects of CK2 inhibition were observed in normal mononuclear blood cells from healthy donors and BCR-ABL negative HL60 cell line. Our data indicate that CK2 kinase supports CML cell viability even in cells with different mechanisms of resistance to TKI, and thus represents a potential target for treatment.
Global analysis of putative phospholipases in the malaria parasite Plasmodium falciparum reveals critical factors for parasite proliferation
Authors: Burda Paul-Christian , Ramaprasad Abhinay , Pietsch Emma , Bielfeld Sabrina , Söhnchen Christoph , Wilcke Louisa , Strauss Jan , Schwudke Dominik , Sait Aaron , Collinson Lucy M , Blackman Michael J , Gilberger Tim-Wolf 
Published: June 2021

ABSTRACTFor its replication within red blood cells, the malaria parasite is highly dependent on correctly regulated lipid metabolism. Enzymes involved in lipid metabolic processes are therefore potential drug targets. We here provide a functional analysis of the 20 putative phospholipases that are expressed by asexual blood stages of Plasmodium falciparum. We reveal a high level of redundancy among members of this group, but using conditional mislocalization and gene disruption techniques we show that the phosphoinositide-specific phospholipase C (PF3D7_1013500) has a previously unrecognized essential role in intracellular parasite maturation. In addition, we demonstrate that the patatin-like phospholipase PF3D7_1358000 localizes to the mitochondrion. Parasites lacking this enzyme display a severe growth phenotype and defects in mitochondrial morphogenesis and function leading to hypersensitivity towards proguanil and inhibitors of the mitochondrial electron transport chain including atovaquone. This demonstrates that regulated mitochondrial lipid homeostasis is necessary for mitochondrial function and coordinated division during parasite multiplication.
Identification and verification of the potential effect of therapeutic miRNA-mRNA pairs on ferroptosis in small cell lung cancer by bioinformatics analysis
Authors: Wu Yuefeng 
Published: June 2021

AbstractOwing to the high mortality rate of small cell lung cancer (SCLC), it is essential to determine a novel therapeutic approach for treating patients with SCLC. miRNA is a type of non-coding RNA that plays a role in translational control. By applying this identity, it is applicable for treating patients using miRNA and nanotechnology. Ferroptosis is a newly discovered type of programmed cell death. Accumulated evidence suggests the possibility of using ferroptosis in treating patients with SCLC. Thus, identifying potential therapeutic miRNA-mRNA pairs that have an impact on ferroptosis will be valuable. In the in silico analysis, several Gene Expression Omnibus datasets were analyzed. The results were verified using other data. Here, we report that the miR-30 family and KIF11 pair have a crucial influence on SCLC cells, which may also affect ferroptosis.
Regulation of Myoepithelial Differentiation in 3-Dimensional Culture
Authors: Thiemann Renee F. , Varney Scott , Moskwa Nicholas , Lamar John , Larsen Melinda , LaFlamme Susan E. 
Published: June 2021

AbstractThe salivary gland can be permanently impaired by radiation treatment for head and neck cancers. Efforts at tissue regeneration have focused on saliva-producing acinar cells. However, myoepithelial cells are also critical to gland function, but mechanisms that regulate their differentiation are poorly defined. To study myoepithelial differentiation, we employed mSG-PAC1 murine salivary gland epithelial cells. We demonstrate that mSG-PAC1 spheroids exhibit phenotypic plasticity between pro-acinar and myoepithelial cell fates. Increased expression of pro-acinar/acinar or myoepithelial RNAs was identified from spheroids cultured under different media conditions by microarray followed by gene-set enrichment analysis. Spheroids cultured with different medium components expressed proteins typical of either acinar or myoepithelial cells, as detected by immunocytochemistry. We demonstrate that the pattern of TAZ expression in the epithelial compartment of the differentiating murine salivary gland correlates with the expression of the myoepithelial marker alpha-SMA, as is the case for TAZ expression in mSG-PAC1 spheroids. Our analysis also indicates that YAP/TAZ target genes are upregulated together with myoepithelial markers. Importantly, siRNA targeting of TAZ expression in mSG-PAC1 spheroids diminished the expression of myoepithelial markers. Our results in thisin vitrocell model implicate TAZ signaling in myoepithelial differentiation.
Assessment of Molecular Mechanics-based Zn2+ Models in Mono- and Bimetallic Ligand Binding Sites
Authors: Melse Okke , Antes Iris 
Published: June 2021

AbstractZn2+ ions play an important role in biology, but accurate sampling of metalloproteins using Molecular Mechanics remains challenging. Several models have been proposed to describe Zn2+ in biomolecular simulations, ranging from nonbonded models, employing classical 12-6 Lennard-Jones (LJ) potentials or extended LJ-potentials, to dummy-atom models and bonded models. We evaluated the performance of a large variety of these Zn2+ models in two challenging environments for which little is known about the performance of these methods, namely in a monometallic (Carbonic Anhydrase II) and a bimetallic ligand binding site (metallo-β-lactamase VIM-2). We focused on properties which are important for a stable, correct binding site description during molecular dynamics (MD) simulations, because a proper treatment of the metal coordination and forces are here essential. We observed that the strongest difference in performance of these Zn2+ models can be found in the description of interactions between Zn2+ and non-charged ligating atoms, such as the imidazole nitrogen in histidine residues. We further show that the nonbonded (12-6 LJ) models struggle most in the description of Zn2+-biomolecule interactions, while the inclusion of ion-induced dipole effects strongly improves the description between Zn2+ and non-charged ligating atoms. The octahedral dummy-atom models result in highly stable simulations and correct Zn2+ coordination, and are therefore highly suitable for binding sites containing an octahedral coordinated Zn2+ ion. The results from this evaluation study in ligand binding sites can guide structural studies of Zn2+ containing proteins, such as MD-refinement of docked ligand poses and long-term MD simulations.
Glypican-6 deficiency causes dose-dependent conotruncal congenital heart malformations through abnormal remodelling of the endocardial cushions
Authors: Tenin Gennadiy , Crozier Alexander , Hentges Kathryn E. , Keavney Bernard 
Published: June 2021

AbstractTetralogy of Fallot (TOF) is considered to be the commonest type of cyanotic congenital heart disease (CHD). A previous GWAS showed significant association between TOF and single nucleotide polymorphisms in chromosome 13q31. Here through integration of population genomic and chromosomal interaction data we identify the heparan sulfate proteoglycan glypican-6 (GPC6) as the potentially responsible gene at the associated locus. We showed that GPC6 is expressed in the endocardial cushions at the appropriate time in development to contribute to TOF risk. We generated mice homozygous for a Gpc6 KO allele, which exhibit 100% neonatal lethality with severe cardiac malformations, namely TOF-type double outlet right ventricle (DORV) with rightward mal-positioned aorta and perimembranous ventricular septal defect (VSD), together with right ventricular (RV) hypertrophy and narrowing of the pulmonary artery. We established a dose-response relationship between Gpc6 expression and the anatomical severity of cardiac malformations. We showed the mouse knockout phenotype arises from abnormal morphology of the endocardial cushions, and tissue-specific knockout of Gpc6 in endothelial and neural crest cell lineages produces a phenotype featuring VSD and aortic malposition analogous to human TOF. This successful identification of a CHD gene from GWAS data suggests that larger GWA studies may find additional causative genes.
DNA METHYLTRANSFERASE 3 (MET3) is regulated by Polycomb Group complex during Arabidopsis endosperm development
Authors: Tirot Louis , Jullien Pauline E. 
Published: June 2021

AbstractComplex epigenetic changes occur during plant reproduction. These regulations ensure the proper transmission of epigenetic information as well as allowing for zygotic totipotency. In Arabidopsis, the main DNA methyltransferase is called MET1 and is responsible for methylating cytosine in the CG context. The Arabidopsis genome encodes for three additional reproduction-specific homologs of MET1, namely MET2a, MET2b and MET3. In this paper, we show that the DNA methyltransferase MET3 is expressed in the seed endosperm and its expression is further restricted to the chalazal endosperm. MET3 is biallelically expressed in the endosperm but displays a paternal expression bias. We found that MET3 expression is regulated by the Polycomb complex proteins FIE and MSI1. Seed development is not impaired in met3 mutant, and we could not observe significant transcriptional changes in met3 mutant. Interestingly, we found that MET3 regulates gene expression in a Polycomb mutant background suggesting a further complexification of the interplay between H3K27me3 and DNA methylation in the seed endosperm.Key messageThe DNA METHYLTRANSFERASE MET3 is controlled by Polycomb group complex during endosperm development.
A wavelet method for solving Caputo–Hadamard fractional differential equation
Authors: Saeed Umer 
Published: June 2021

PurposeThe purpose of the present work is to propose a wavelet method for the numerical solutions of Caputo–Hadamard fractional differential equations on any arbitrary interval.Design/methodology/approachThe author has modified the CAS wavelets (mCAS) and utilized it for the solution of Caputo–Hadamard fractional linear/nonlinear initial and boundary value problems. The author has derived and constructed the new operational matrices for the mCAS wavelets. Furthermore, The author has also proposed a method which is the combination of mCAS wavelets and quasilinearization technique for the solution of nonlinear Caputo–Hadamard fractional differential equations.FindingsThe author has proved the orthonormality of the mCAS wavelets. The author has constructed the mCAS wavelets matrix, mCAS wavelets operational matrix of Hadamard fractional integration of arbitrary order and mCAS wavelets operational matrix of Hadamard fractional integration for Caputo–Hadamard fractional boundary value problems. These operational matrices are used to make the calculations fast. Furthermore, the author works out on the error analysis for the method. The author presented the procedure of implementation for both Caputo–Hadamard fractional initial and boundary value problems. Numerical simulation is provided to illustrate the reliability and accuracy of the method.Originality/valueMany scientist, physician and engineers can take the benefit of the presented method for the simulation of their linear/nonlinear Caputo–Hadamard fractional differential models. To the best of the author’s knowledge, the present work has never been proposed and implemented for linear/nonlinear Caputo–Hadamard fractional differential equations.
Flow control in microfluidics devices: electro-osmotic Couette flow with joule heating effect
Authors: Ahamed Saleel C. , Alshahrani Saad Ayed , Afzal Asif , Baig Maughal Ahmed Ali , Kamangar Sarfaraz , Yunus Khan T.M. 
Published: June 2021

PurposeJoule heating effect is a pervasive phenomenon in electro-osmotic flow because of the applied electric field and fluid electrical resistivity across the microchannels. Its effect in electro-osmotic flow field is an important mechanism to control the flow inside the microchannels and it includes numerous applications.Design/methodology/approachThis research article details the numerical investigation on alterations in the profile of stream wise velocity of simple Couette-electroosmotic flow and pressure driven electro-osmotic Couette flow by the dynamic viscosity variations happened due to the Joule heating effect throughout the dielectric fluid usually observed in various microfluidic devices.FindingsThe advantages of the Joule heating effect are not only to control the velocity in microchannels but also to act as an active method to enhance the mixing efficiency. The results of numerical investigations reveal that the thermal field due to Joule heating effect causes considerable variation of dynamic viscosity across the microchannel to initiate a shear flow when EDL (Electrical Double Layer) thickness is increased and is being varied across the channel.Originality/valueThis research work suggest how joule heating can be used as en effective mechanism for flow control in microfluidic devices.