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https://www.readbyqxmd.com/read/29346564/genome-wide-comparison-of-allele-specific-gene-expression-between-african-and-european-populations
#1
Lei Tian, Asifullah Khan, Zhilin Ning, Kai Yuan, Chao Zhang, Haiyi Lou, Yuan Yuan, Shuhua Xu
Transcriptomic diversity across human populations reflects differential regulatory mechanisms. Allelic-imbalanced gene expression is a genetic regulatory mechanism that contributes to human phenotypic variation. To systematically investigate genome-wide allele-specific expression (ASE), we analyzed RNA-Seq data from European and African populations provided by the Geuvadis project. We identified 17 sites in 13 genes showing ASE in both Europeans and Africans, and 19 sites in 18 genes showing population-specific ASE, including both novel and known ASE signals...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346514/optimal-water-networks-in-protein-cavities-with-gasol-and-3d-rism
#2
Lucia Fusani, Ian Wall, David Palmer, Alvaro Cortes
Motivation: Water molecules in protein binding sites play essential roles in biological processes. The popular 3D-RISM prediction method can calculate the solvent density distribution within minutes, but is difficult to convert it into explicit water molecules. Results: We present GAsol, a tool that is capable of finding the network of water molecules that best fits a particular 3D-RISM density distribution in a fast and accurate manner and that outperforms other available tools by finding the globally optimal solution thanks to its genetic algorithm...
January 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29346402/gene-regulation-in-kluyveromyces-marxianus-in-the-context-of-chromosomes
#3
Du Toit W P Schabort, Stephanus G Kilian, James C du Preez
Eukaryotes, including the unicellular eukaryotes such as yeasts, employ multiple levels of gene regulation. Regulation of chromatin structure through chromatin compaction cascades, and influenced by transcriptional insulators, might play a role in the coordinated regulation of genes situated at adjacent loci and expressed as a co-regulated cluster. Subtelomeric gene silencing, which has previously been described in the yeast Saccharomyces cerevisiae, is an example of this phenomenon. Transcription from a common regulatory element located around a shared intergenic region is another factor that could coordinate the transcription of genes at adjacent loci...
2018: PloS One
https://www.readbyqxmd.com/read/29346371/identification-of-novel-leishmanicidal-molecules-by-virtual-and-biochemical-screenings-targeting-leishmania-eukaryotic-initiation-factor-4a
#4
Emna Harigua-Souiai, Yosser Zina Abdelkrim, Imen Bassoumi-Jamoussi, Ons Zakraoui, Guillaume Bouvier, Khadija Essafi-Benkhadir, Josette Banroques, Nathan Desdouits, Hélène Munier-Lehmann, Mourad Barhoumi, N Kyle Tanner, Michael Nilges, Arnaud Blondel, Ikram Guizani
Leishmaniases are neglected parasitic diseases in spite of the major burden they inflict on public health. The identification of novel drugs and targets constitutes a research priority. For that purpose we used Leishmania infantum initiation factor 4A (LieIF), an essential translation initiation factor that belongs to the DEAD-box proteins family, as a potential drug target. We modeled its structure and identified two potential binding sites. A virtual screening of a diverse chemical library was performed for both sites...
January 18, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29346132/enzymatic-sources-and-physio-pathological-functions-of-soluble-pro-renin-receptor
#5
Qing Zhu, Tianxin Yang
PURPOSE OF REVIEW: (Pro)renin receptor (PRR) belongs to type I transmembrane receptor family and binds both prorenin and renin, representing a potential regulator of the activity of the renin-angiotensin system. Soluble form of PRR (sPRR) is generated by intracellular protease-mediated cleavage of full-length PRR. The purpose of this review is to highlight recent advances in understanding the mechanisms of action and production of sPRR. RECENT FINDINGS: It has recently been demonstrated that site-1-protease (S1P) plays a dominant role in the generation of sPRR...
January 16, 2018: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/29346073/extensive-conservation-of-prokaryotic-ribosomal-binding-sites-in-known-and-novel-picobirnaviruses
#6
Siddharth R Krishnamurthy, David Wang
Currently, the Leviviridae and Cystoviridae are the only two recognized families of prokaryotic RNA viruses. Picobirnaviruses, which are bisegmented double-stranded RNA viruses commonly found in animal stool samples, are currently thought to be animal viruses, but have not been propagated in cell culture or in an animal model. We hypothesize that picobirnaviruses are prokaryotic RNA viruses. We identified and analyzed the genomes of 38 novel picobirnaviruses and determined that a classical bacterial sequence motif, the ribosomal binding site (RBS), is present in the 5' untranslated regions (5' UTRs) of all of the novel as well as all previously published picobirnavirus sequences...
January 12, 2018: Virology
https://www.readbyqxmd.com/read/29346072/synthesis-biological-evaluation-and-molecular-docking-studies-of-novel-benzimidazole-derivatives
#7
Gagandeep Singh, Amanjot Singh, Raman K Verma, Rajiv Mall, Uzma Azeem
A novel series of N-substituted-benzimidazolyl linked para substituted benzylidene based molecules containing three pharmacologically potent hydrogen bonding parts namely; 2,4-thiazolidinedione (TZD: a 2,4-dicarbonyl), diethyl malonate (DEM: a 1,3-diester and an isooxazolidinedione analog) and methyl acetoacetate (MAA: a β-ketoester) (6a-11b) were synthesized and evaluated for in vitro α-glucosidase inhibition. The structure of the novel synthesized compounds was confirmed through the spectral studies (LC-MS, 1H NMR, 13C NMR, FT-IR)...
December 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29346071/identification-of-potential-inhibitors-against-nuclear-dam1-complex-subunit-ask1-of-candida-albicans-using-virtual-screening-and-md-simulations
#8
Himanshu Tripathi, Feroz Khan
Identification of hit compounds against specific target form the starting point for a drug discovery program. A consistent decline of new chemical entities (NCEs) in recent years prompted a challenge to explore newer approaches to discover potential hit compounds that in turn can be converted into leads, and ultimately drug with desired therapeutic efficacy. The vast amount of omics and activity data available in public databases offers an opportunity to identify novel targets and their potential inhibitors...
January 1, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29345921/molecular-mechanisms-in-the-selectivity-of-non-steroidal-anti-inflammatory-drugs
#9
Yasmin Shamsudin Khan, Hugo Gutiérrez de Terán, Johan Åqvist
Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX) 1 and 2 with varying degrees of selectivity. A group of COX-2 selective inhibitors - coxibs - bind in a time-dependent manner through a three-step mechanism, utilizing a side-pocket in the binding site. Coxibs have been extensively probed to identify the structural features regulating the slow tight-binding mechanism responsible for COX-2 selectivity. In this study, we further probe a structurally and kinetically diverse data set of COX inhibitors in COX-2 by molecular dynamics and free energy simulations...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345908/a-small-molecule-inhibitor-of-human-dna-polymerase-eta-potentiates-the-effects-of-cisplatin-in-tumor-cells
#10
Maroof K Zafar, Leena Maddukuri, Amit Ketkar, Narsimha Penthala, Megan R Reed, Sarah D Eddy, Peter A Crooks, Robert L Eoff
Translesion DNA synthesis (TLS) performed by human DNA polymerase eta (hpol η) allows tolerance of damage from cis-diamminedichloroplatinum(II) (CDDP or cisplatin). We have developed hpol η inhibitors derived from N-aryl-substituted indole barbituric acid (IBA), indole thiobarbituric acid (ITBA), and indole quinuclidine scaffolds and identified 5-((5-chloro-1-(naphthalen-2-ylmethyl)-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione (PNR-7-02), an ITBA derivative that inhibited hpol η activity with an IC50 value of 8 μM and exhibited five- to ten-fold specificity for hpol η over replicative pols...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345384/a-single-molecule-propyne-trap-highly-efficient-removal-of-propyne-from-propylene-with-anion-pillared-ultramicroporous-materials
#11
Lifeng Yang, Xili Cui, Qiwei Yang, Siheng Qian, Hui Wu, Zongbi Bao, Zhiguo Zhang, Qilong Ren, Wei Zhou, Banglin Chen, Huabin Xing
Propyne/propylene (C3 H4 /C3 H6 ) separation is a critical process for the production of polymer-grade C3 H6 . However, optimization of the structure of porous materials for the highly efficient removal of C3 H4 from C3 H6 remains challenging due to their similar structures and ultralow C3 H4 concentration. Here, it is first reported that hybrid ultramicroporous materials with pillared inorganic anions (SiF62- = SIFSIX, NbOF52- = NbOFFIVE) can serve as highly selective C3 H4 traps for the removal of trace C3 H4 from C3 H6 ...
January 18, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29345372/truncation-of-neurokinin-1-receptor-negative-regulation-of-substance-p-signaling
#12
REVIEW
Sergei Spitsin, Vasiliki Pappa, Steven D Douglas
Substance P (SP) is a tachykinin peptide, which triggers intracellular signaling in the nervous and immune systems, as well as, other local and systemic events. The interaction between SP and its receptor, neurokinin-1 receptor (NK1R), results in major downstream cellular actions, which include changes in calcium fluxes, ERK, and p21-activated kinase phosphorylation and NFκB activation. Two naturally occurring variants of the NK1R, the full-length, 407 aa receptor (NK1R-F) and the truncated, 311 aa isoform (NK1R-T), mediate the actions of SP...
January 10, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29345346/galectin-3-type-c-self-association-on-neutrophil-surfaces-the-carbohydrate-recognition-domain-regulates-cell-function
#13
Martina Sundqvist, Amanda Welin, Jonas Elmwall, Veronica Osla, Ulf J Nilsson, Hakon Leffler, Johan Bylund, Anna Karlsson
Galectin-3 is an endogenous β-galactoside-binding lectin comprising a carbohydrate recognition domain (CRD) linked to a collagen-like N-domain. Both domains are required for galectin-3 to induce cellular effects; a C-terminal fragment of galectin-3, galectin-3C, containing the CRD but lacking the N-domain, binds cell surface glycoconjugates but does not induce cellular effects since cross-linking promoted by the N-domain is thought to be required. Instead, galectin-3C is proposed to antagonize the effects of galectin-3 by competing for binding sites...
January 10, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29345294/hypoxia-stimulates-the-cytoplasmic-localization-of-oncogenic-long-noncoding-rna-linc00152-in-colorectal-cancer
#14
Yujiro Nishizawa, Masamitsu Konno, Ayumu Asai, Jun Koseki, Koichi Kawamoto, Norikatsu Miyoshi, Hidekazu Takahashi, Naohiro Nishida, Naotsugu Haraguchi, Daisuke Sakai, Toshihiro Kudo, Taishi Hata, Chu Matsuda, Tsunekazu Mizushima, Taroh Satoh, Yuichiro Doki, Masaki Mori, Hideshi Ishii
Recent studies have indicated that long noncoding RNAs (lncRNAs) play a pivotal role in almost all physiological cellular processes, including every stage of cancer development. Given that hypoxia in the tumor microenvironment is involved in the malignant behavior of tumors, such as invasion and metastasis, we investigated the cytoplasmic and nuclear localization of lncRNAs in colorectal cancer cells. A cell culture under hypoxic conditions revealed several lncRNAs, such as LINC00152, whose levels were increased in the cytoplasm of colorectal cancer cells...
February 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29345110/remarkable-similarity-in-plasmodium-falciparum-and-plasmodium-vivax-geranylgeranyl-diphosphate-synthase-ggpps-dynamics-and-its-implication-for-anti-malarial-drug-design
#15
Aishwarya Venkatramani, Clarisse G Ricci, Eric Oldfield, J Andrew McCammon
Malaria, mainly caused by Plasmodium falciparum and Plasmodium vivax, has been a growing cause of morbidity and mortality. P. falciparum is more lethal than is P. vivax, but there is a vital need for effective drugs against both species. Geranylgeranyl diphosphate synthase (GGPPS) is an enzyme involved in the biosynthesis of quinones and in protein prenylation, and has been proposed to be a malaria drug target. However, the structure of P. falciparum GGPPS (PfGGPPS) has not been determined, due to difficulties in crystallization...
January 18, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29344585/hereditary-folate-malabsorption-due-to-a-mutation-in-the-external-gate-of-the-proton-coupled-folate-transporter-slc46a1
#16
Srinivas Aluri, Rongbao Zhao, Charlotte Lubout, Susanna M I Goorden, Andras Fiser, I David Goldman
Hereditary folate malabsorption (HFM) is an autosomal recessive disorder characterized by impaired intestinal folate absorption and impaired folate transport across the choroid plexus due to loss of function of the proton-coupled folate transporter (PCFT-SLC46A1). We report a novel mutation, causing HFM, affecting a residue located in the 11th transmembrane helix within the external gate. The mutant N411K-PCFT was stable, trafficked to the cell membrane, and had sufficient residual activity to characterize the transport defect and the structural requirements at this site for gate function...
January 9, 2018: Blood Advances
https://www.readbyqxmd.com/read/29344581/glycophorin-c-sialylation-regulates-lu-bcam-adhesive-capacity-during-erythrocyte-aging
#17
T R L Klei, D Z de Back, P J Asif, P J J H Verkuijlen, M Veldthuis, P C Ligthart, J Berghuis, E Clifford, B M Beuger, T K van den Berg, R van Zwieten, W El Nemer, R van Bruggen
Lutheran/basal cell adhesion molecule (Lu/BCAM) is a transmembrane adhesion molecule expressed by erythrocytes and endothelial cells that can interact with the extracellular matrix protein laminin-α5. In sickle cell disease, Lu/BCAM is thought to contribute to adhesion of sickle erythrocytes to the vascular wall, especially during vaso-occlusive crises. On healthy erythrocytes however, its function is unclear. Here we report that Lu/BCAM is activated during erythrocyte aging. We show that Lu/BCAM-mediated binding to laminin-α5 is restricted by interacting, in cis, with glycophorin-C-derived sialic acid residues...
January 9, 2018: Blood Advances
https://www.readbyqxmd.com/read/29344310/drug-repurposing-screening-identifies-tioconazole-as-an-atg4-inhibitor-that-suppresses-autophagy-and-sensitizes-cancer-cells-to-chemotherapy
#18
Pei-Feng Liu, Kun-Lin Tsai, Chien-Jen Hsu, Wei-Lun Tsai, Jin-Shiung Cheng, Hsueh-Wei Chang, Chung-Wai Shiau, Yih-Gang Goan, Ho-Hsing Tseng, Chih-Hsuan Wu, John C Reed, Lee-Wei Yang, Chih-Wen Shu
Background: Tumor cells require proficient autophagy to meet high metabolic demands and resist chemotherapy, which suggests that reducing autophagic flux might be an attractive route for cancer therapy. However, this theory in clinical cancer research remains controversial due to the limited number of drugs that specifically inhibit autophagy-related (ATG) proteins. Methods: We screened FDA-approved drugs using a novel platform that integrates computational docking and simulations as well as biochemical and cellular reporter assays to identify potential drugs that inhibit autophagy-required cysteine proteases of the ATG4 family...
2018: Theranostics
https://www.readbyqxmd.com/read/29344296/cdk16-phosphorylates-and-degrades-p53-to-promote-radioresistance-and-predicts-prognosis-in-lung-cancer
#19
Jie Xie, Yan Li, Ke Jiang, Kaishun Hu, Sheng Zhang, Xiaorong Dong, Xiaofang Dai, Li Liu, Tao Zhang, Kunyu Yang, Kai Huang, Junjie Chen, Shaojun Shi, Yu Zhang, Gang Wu, Shuangbing Xu
Rationale: Radioresistance is considered the main cause of local relapse in lung cancer. However, the molecular mechanisms of radioresistance remain poorly understood. This study investigates the role of CDK16 in radioresistance of human lung cancer cells. Methods: The expression levels of CDK16 were determined by immunohistochemistry in lung cancer tissues and adjacent normal lung tissues. Immunoprecipitation assay and GST pulldown were utilized to detect the protein-protein interaction. The phosphorylation of p53 was evaluated by in vitro kinase assay...
2018: Theranostics
https://www.readbyqxmd.com/read/29344170/phosphorylation-of-ser6-in-hnrnpa1-by-s6k2-regulates-glucose-metabolism-and-cell-growth-in-colorectal-cancer
#20
Yan Sun, Man Luo, Guilin Chang, Weiying Ren, Kefen Wu, Xi Li, Jiping Shen, Xiaoping Zhao, Yu Hu
Abnormal glucose metabolism is critical in colorectal cancer (CRC) development. Expression of the pyruvate kinase (PK) M2 isoform, rather than the PKM1 isoform, serves important functions in reprogramming the glucose metabolism of cancer cells. Preferential expression of PKM2 is primarily driven by alternative splicing, which is coordinated by a group of splicing factors including heterogeneous nuclear ribonucleoprotein (hnRNP)A1, hnRNPA2 and RNA binding motif containing. However, the underlying molecular mechanisms associated with cancer cell expression of PKM2, instead of PKM1, remain unknown...
December 2017: Oncology Letters
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