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World Journal of Biological Chemistry

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https://www.readbyqxmd.com/read/27621770/chromatin-boundary-elements-organize-genomic-architecture-and-developmental-gene-regulation-in-drosophila-hox-clusters
#1
REVIEW
Zhibo Ma, Mo Li, Sharmila Roy, Kevin J Liu, Matthew L Romine, Derrick C Lane, Sapna K Patel, Haini N Cai
The three-dimensional (3D) organization of the eukaryotic genome is critical for its proper function. Evidence suggests that extensive chromatin loops form the building blocks of the genomic architecture, separating genes and gene clusters into distinct functional domains. These loops are anchored in part by a special type of DNA elements called chromatin boundary elements (CBEs). CBEs were originally found to insulate neighboring genes by blocking influences of transcriptional enhancers or the spread of silent chromatin...
August 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27247709/high-mobility-group-protein-1-a-collaborator-in-nucleosome-dynamics-and-estrogen-responsive-gene-expression
#2
REVIEW
William M Scovell
High mobility group protein 1 (HMGB1) is a multifunctional protein that interacts with DNA and chromatin to influence the regulation of transcription, DNA replication and repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, adenosine triphosphate-independent manner. As a result, the canonical nucleosome is converted to two stable, physically distinct nucleosome conformers. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding...
May 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981207/epigenetic-alteration-to-activate-bmp2-smad-signaling-in-raf-induced-senescence
#3
Mai Fujimoto, Yasunobu Mano, Motonobu Anai, Shogo Yamamoto, Masaki Fukuyo, Hiroyuki Aburatani, Atsushi Kaneda
AIM: To investigate epigenomic and gene expression alterations during cellular senescence induced by oncogenic Raf. METHODS: Cellular senescence was induced into mouse embryonic fibroblasts (MEFs) by infecting retrovirus to express oncogenic Raf (RafV600E). RNA was collected from RafV600E cells as well as MEFs without infection and MEFs with mock infection, and a genome-wide gene expression analysis was performed using microarray. The epigenomic status for active H3K4me3 and repressive H3K27me3 histone marks was analyzed by chromatin immunoprecipitation-sequencing for RafV600E cells on day 7 and for MEFs without infection...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981206/high-levels-of-homocysteine-downregulate-apolipoprotein-e-expression-via-nuclear-factor-kappa-b
#4
Violeta G Trusca, Adina D Mihai, Elena V Fuior, Ioana M Fenyo, Anca V Gafencu
AIM: To investigate the effect of high homocysteine (Hcy) levels on apolipoprotein E (apoE) expression and the signaling pathways involved in this gene regulation. METHODS: Reverse transcriptase polymerase chain reaction (RT-PCR) and Western blot were used to assess apoE expression in cells treated with various concentrations (50-500 μmol/L) of Hcy. Calcium phosphate-transient transfections were performed in HEK-293 and RAW 264.7 cells to evaluate the effect of Hcy on apoE regulatory elements [promoter and distal multienhancer 2 (ME2)]...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981205/arctic-ground-squirrel-neuronal-progenitor-cells-resist-oxygen-and-glucose-deprivation-induced-death
#5
Kelly L Drew, Matthew Wells, Rebecca McGee, Austin P Ross, Judith Kelleher-Andersson
AIM: To investigate the influence of ischemia/reperfusion on arctic ground squirrel (AGS) neuronal progenitor cells (NPCs), we subjected these cultured cells to oxygen and glucose deprivation. METHODS: AGS NPCs were expanded and differentiated into NPCs and as an ischemia vulnerable control, commercially available human NPCs (hNPCs) were seeded from thawed NPCs. NPCs, identified by expression of TUJ1 were seen at 14-21 d in vitro (DIV). Cultures were exposed to control conditions, hypoxia, oxygen and glucose deprivation or glucose deprivation alone or following return to normal conditions to model reperfusion...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981204/engineered-magnetic-core-shell-nanoprobes-synthesis-and-applications-to-cancer-imaging-and-therapeutics
#6
REVIEW
Samir Mandal, Keya Chaudhuri
Magnetic core shell nanoparticles are composed of a highly magnetic core material surrounded by a thin shell of desired drug, polymer or metal oxide. These magnetic core shell nanoparticles have a wide range of applications in biomedical research, more specifically in tissue imaging, drug delivery and therapeutics. The present review discusses the up-to-date knowledge on the various procedures for synthesis of magnetic core shell nanoparticles along with their applications in cancer imaging, drug delivery and hyperthermia or cancer therapeutics...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981203/regulation-of-rna-binding-proteins-in-trypanosomatid-protozoan-parasites
#7
REVIEW
María Albertina Romaniuk, Gabriela Cervini, Alejandro Cassola
Posttranscriptional mechanisms have a critical role in the overall outcome of gene expression. These mechanisms are especially relevant in protozoa from the genus Trypanosoma, which is composed by death threatening parasites affecting people in Sub-saharan Africa or in the Americas. In these parasites the classic view of regulation of transcription initiation to modulate the products of a given gene cannot be applied. This is due to the presence of transcription start sites that give rise to long polycistronic units that need to be processed costranscriptionally by trans-splicing and polyadenylation to give mature monocistronic mRNAs...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981202/development-of-regional-specificity-of-spinal-and-medullary-dorsal-horn-neurons
#8
REVIEW
Yu-Feng Xie, Xing-Hong Jiang, Barry J Sessle, Xian-Min Yu
Extensive studies have focused on the development and regionalization of neurons in the central nervous system (CNS). Many genes, which play crucial roles in the development of CNS neurons, have been identified. By using the technique "direct reprogramming", neurons can be produced from multiple cell sources such as fibroblasts. However, understanding the region-specific regulation of neurons in the CNS is still one of the biggest challenges in the research field of neuroscience. Neurons located in the trigeminal subnucleus caudalis (Vc) and in the spinal dorsal horn (SDH) play crucial roles in pain and sensorimotor functions in the orofacial and other somatic body regions, respectively...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981201/api2-malt1-oncoprotein-promotes-lymphomagenesis-via-unique-program-of-substrate-ubiquitination-and-proteolysis
#9
REVIEW
Shaun Rosebeck, Megan S Lim, Kojo S J Elenitoba-Johnson, Linda M McAllister-Lucas, Peter C Lucas
Lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) is the most common extranodal B cell tumor and accounts for 8% of non-Hodgkin's lymphomas. Gastric MALT lymphoma is the best-studied example and is a prototypical neoplasm that occurs in the setting of chronic inflammation brought on by persistent infection or autoimmune disease. Cytogenetic abnormalities are commonly acquired during the course of disease and the most common is chromosomal translocation t(11;18)(q21;q21), which creates the API2-MALT1 fusion oncoprotein...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981200/longevity-of-animals-under-reactive-oxygen-species-stress-and-disease-susceptibility-due-to-global-warming
#10
REVIEW
Biswaranjan Paital, Sumana Kumari Panda, Akshaya Kumar Hati, Bobllina Mohanty, Manoj Kumar Mohapatra, Shyama Kanungo, Gagan Bihari Nityananda Chainy
The world is projected to experience an approximate doubling of atmospheric CO2 concentration in the next decades. Rise in atmospheric CO2 level as one of the most important reasons is expected to contribute to raise the mean global temperature 1.4 °C-5.8 °C by that time. A survey from 128 countries speculates that global warming is primarily due to increase in atmospheric CO2 level that is produced mainly by anthropogenic activities. Exposure of animals to high environmental temperatures is mostly accompanied by unwanted acceleration of certain biochemical pathways in their cells...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981199/recent-advances-in-production-purification-and-applications-of-phycobiliproteins
#11
REVIEW
Ravi Raghav Sonani, Rajesh Prasad Rastogi, Rutvij Patel, Datta Madamwar
An obligatory sunlight requirement for photosynthesis has exposed cyanobacteria to different quantity and quality of light. Cyanobacteria can exhibit efficient photosynthesis over broad region (450 to 650 nm) of solar spectrum with the help of brilliantly coloured pigment proteins called phycobiliproteins (PBPs). Besides light-harvesting, PBPs are found to involve in several life sustaining phenomena including photoprotection in cyanobacteria. The unique spectral features (like strong absorbance and fluorescence), proteineous nature and, some imperative properties like hepato-protective, anti-oxidants, anti-inflammatory and anti-aging activity of PBPs enable their use in food, cosmetics, pharmaceutical and biomedical industries...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981198/understanding-the-molecular-mechanisms-of-cancer-prevention-by-dietary-phytochemicals-from-experimental-models-to-clinical-trials
#12
REVIEW
Girish B Maru, Rasika R Hudlikar, Gaurav Kumar, Khushboo Gandhi, Manoj B Mahimkar
Chemoprevention is one of the cancer prevention approaches wherein natural/synthetic agent(s) are prescribed with the aim to delay or disrupt multiple pathways and processes involved at multiple steps, i.e., initiation, promotion, and progression of cancer. Amongst environmental chemopreventive compounds, diet/beverage-derived components are under evaluation, because of their long history of exposure to humans, high tolerability, low toxicity, and reported biological activities. This compilation briefly covers and compares the available evidence on chemopreventive efficacy and probable mechanism of chemoprevention by selected dietary phytochemicals (capsaicin, curcumin, diallyl sulphide, genistein, green/black tea polyphenols, indoles, lycopene, phenethyl isocyanate, resveratrol, retinoids and tocopherols) in experimental systems and clinical trials...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981197/rna-binding-proteins-related-to-stress-response-and-differentiation-in-protozoa
#13
REVIEW
Lysangela Ronalte Alves, Samuel Goldenberg
RNA-binding proteins (RBPs) are key regulators of gene expression. There are several distinct families of RBPs and they are involved in the cellular response to environmental changes, cell differentiation and cell death. The RBPs can differentially combine with RNA molecules and form ribonucleoprotein (RNP) complexes, defining the function and fate of RNA molecules in the cell. RBPs display diverse domains that allow them to be categorized into distinct families. They play important roles in the cellular response to physiological stress, in cell differentiation, and, it is believed, in the cellular localization of certain mRNAs...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981196/dynamic-interplay-between-adhesion-surfaces-in-carcinomas-cell-cell-and-cell-matrix-crosstalk
#14
REVIEW
Yvonne E Smith, Sri HariKrishna Vellanki, Ann M Hopkins
Cell-cell and cell-matrix signaling and communication between adhesion sites involve mechanisms which are required for cellular functions during normal development and homeostasis; however these cellular functions and mechanisms are often deregulated in cancer. Aberrant signaling at cell-cell and cell-matrix adhesion sites often involves downstream mediators including Rho GTPases and tyrosine kinases. This review discusses these molecules as putative mediators of cellular crosstalk between cell-cell and cell-matrix adhesion sites, in addition to their attractiveness as therapeutic targets in cancer...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981195/new-insights-into-sodium-transport-regulation-in-the-distal-nephron-role-of-g-protein-coupled-receptors
#15
REVIEW
Luciana Morla, Aurélie Edwards, Gilles Crambert
The renal handling of Na(+) balance is a major determinant of the blood pressure (BP) level. The inability of the kidney to excrete the daily load of Na(+) represents the primary cause of chronic hypertension. Among the different segments that constitute the nephron, those present in the distal part (i.e., the cortical thick ascending limb, the distal convoluted tubule, the connecting and collecting tubules) play a central role in the fine-tuning of renal Na(+) excretion and are the target of many different regulatory processes that modulate Na(+) retention more or less efficiently...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981194/complexity-of-vitamin-e-metabolism
#16
REVIEW
Lisa Schmölz, Marc Birringer, Stefan Lorkowski, Maria Wallert
Bioavailability of vitamin E is influenced by several factors, most are highlighted in this review. While gender, age and genetic constitution influence vitamin E bioavailability but cannot be modified, life-style and intake of vitamin E can be. Numerous factors must be taken into account however, i.e., when vitamin E is orally administrated, the food matrix may contain competing nutrients. The complex metabolic processes comprise intestinal absorption, vascular transport, hepatic sorting by intracellular binding proteins, such as the significant α-tocopherol-transfer protein, and hepatic metabolism...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26981193/yersinia-type-iii-effectors-perturb-host-innate-immune-responses
#17
REVIEW
Khavong Pha, Lorena Navarro
The innate immune system is the first line of defense against invading pathogens. Innate immune cells recognize molecular patterns from the pathogen and mount a response to resolve the infection. The production of proinflammatory cytokines and reactive oxygen species, phagocytosis, and induced programmed cell death are processes initiated by innate immune cells in order to combat invading pathogens. However, pathogens have evolved various virulence mechanisms to subvert these responses. One strategy utilized by Gram-negative bacterial pathogens is the deployment of a complex machine termed the type III secretion system (T3SS)...
February 26, 2016: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26629323/jak3-inhibitor-vi-is-a-mutant-specific-inhibitor-for-epidermal-growth-factor-receptor-with-the-gatekeeper-mutation-t790m
#18
Naoyuki Nishiya, Yasumitsu Sakamoto, Yusuke Oku, Takamasa Nonaka, Yoshimasa Uehara
AIM: To identify non-quinazoline kinase inhibitors effective against drug resistant mutants of epidermal growth factor receptor (EGFR). METHODS: A kinase inhibitor library was subjected to screening for specific inhibition pertaining to the in vitro kinase activation of EGFR with the gatekeeper mutation T790M, which is resistant to small molecular weight tyrosine kinase inhibitors (TKIs) for EGFR in non-small cell lung cancers (NSCLCs). This inhibitory effect was confirmed by measuring autophosphorylation of EGFR T790M/L858R in NCI-H1975 cells, an NSCLC cell line harboring the gatekeeper mutation...
November 26, 2015: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26629322/dna-microarray-unravels-rapid-changes-in-transcriptome-of-mk-801-treated-rat-brain
#19
Yuka Kobayashi, Sofya P Kulikova, Junko Shibato, Randeep Rakwal, Hiroyuki Satoh, Didier Pinault, Yoshinori Masuo
AIM: To investigate the impact of MK-801 on gene expression patterns genome wide in rat brain regions. METHODS: Rats were treated with an intraperitoneal injection of MK-801 [0.08 (low-dose) and 0.16 (high-dose) mg/kg] or NaCl (vehicle control). In a first series of experiment, the frontoparietal electrocorticogram was recorded 15 min before and 60 min after injection. In a second series of experiments, the whole brain of each animal was rapidly removed at 40 min post-injection, and different regions were separated: amygdala, cerebral cortex, hippocampus, hypothalamus, midbrain and ventral striatum on ice followed by DNA microarray (4 × 44 K whole rat genome chip) analysis...
November 26, 2015: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26629321/connective-tissue-growth-factor-differentially-binds-to-members-of-the-cystine-knot-superfamily-and-potentiates-platelet-derived-growth-factor-b-signaling-in-rabbit-corneal-fibroblast-cells
#20
Liya Pi, Pei-Yu Chung, Sriniwas Sriram, Masmudur M Rahman, Wen-Yuan Song, Edward W Scott, Bryon E Petersen, Gregory S Schultz
AIM: To study the binding of connective tissue growth factor (CTGF) to cystine knot-containing ligands and how this impacts platelet-derived growth factor (PDGF)-B signaling. METHODS: The binding strengths of CTGF to cystine knot-containing growth factors including vascular endothelial growth factor (VEGF)-A, PDGF-B, bone morphogenetic protein (BMP)-4, and transforming growth factor (TGF)-β1 were compared using the LexA-based yeast two-hybrid system. EYG48 reporter strain that carried a wild-type LEU2 gene under the control of LexA operators and a lacZ reporter plasmid (p80p-lacZ) containing eight high affinity LexA binding sites were used in the yeast two-hybrid analysis...
November 26, 2015: World Journal of Biological Chemistry
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