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International Journal of Biochemistry & Cell Biology

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https://www.readbyqxmd.com/read/28082099/a-beginner-s-guide-to-tissue-clearing
#1
Pablo Ariel
The last decade has seen a proliferation of tissue clearing methods that render large biological samples transparent and allow unprecedented three-dimensional views of enormous volumes of tissue. For a scientist wondering whether these methods will be useful to address their research problems, it can be bewildering to sort through the ever-increasing number of papers introducing new clearing methods. Here, I provide a concise summary for the novice describing what tissue clearing is, which research problems it can be applied to, how to decide on a clearing method, and where the field is headed in the future...
January 7, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28065757/fats-for-thoughts-an-update-on-brain-fatty-acid-metabolism
#2
Adele Romano, Justyna Barbara Koczwara, Cristina Anna Gallelli, Daniele Vergara, Maria Vittoria Micioni Di Bonaventura, Silvana Gaetani, Anna Maria Giudetti
Brain fatty acid (FA) metabolism deserves a close attention not only for its energetic aspects but also because FAs and their metabolites/derivatives are able to influence many neural functions, contributing to brain pathologies or representing potential targets for pharmacological and/or nutritional interventions. Glucose is the preferred energy substrate for the brain, whereas the role of FAs is more marginal. In conditions of decreased glucose supply ketone bodies, mainly formed by FA oxidation, are the alternative main energy source...
January 5, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28064010/vascular-endothelial-cells-senescence-is-associated-with-nod-like-receptor-family-pyrin-domain-containing-3-nlrp3-inflammasome-activation-via-reactive-oxygen-species-ros-thioredoxin-interacting-protein-txnip-pathway
#3
Yanlin Yin, Zhihui Zhou, Weiwei Liu, Qun Chang, Guanqun Sun, Yalei Dai
Endothelial dysfunction caused by endothelial cells senescence and chronic inflammation is tightly linked to the development of cardiovascular diseases. NLRP3 (NOD-like receptor family pyrin domain-containing3) inflammasome plays a central role in inflammatory response that is associated with diverse inflammatory diseases. This study explores the effects and possible mechanisms of NLRP3 inflammasome in endothelial cells senescence. Results show an increment of pro-inflammatory cytokine interleukin (IL) -1β secretion and caspase-1 activation during the senescence of endothelial cells induced by bleomycin...
January 4, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28049018/transactivation-of-the-epidermal-growth-factor-receptor-in-responses-to-myocardial-stress-and-cardioprotection
#4
REVIEW
Melissa E Reichelt, Shannon O'Brien, Walter G Thomas, John P Headrick
The epidermal growth factor receptor (EGFR) family comprises the ErbB1 (EGFR) and ErbB4 receptors as well as the 'co-receptors' ErbB2 (which does not bind EGF ligands) and ErbB3 (which lack tyrosine kinase activity). This family of receptors is essential for cardiac development, myocardial, renal and vascular function, and cardiac responses to physiological and pathological perturbations. The EGFR appears critical in protecting cardiac cells from injury, while considerable attention has focussed on neuregulin/ErbB4 signalling in potentially ameliorating cardiomyopathy/heart failure...
December 31, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28040436/fam98a-associates-with-ddx1-c14orf166-fam98b-in-a-novel-complex-involved-in-colorectal-cancer-progression
#5
Khondker Ayesha Akter, Mohammed A Mansour, Toshinori Hyodo, Takeshi Senga
Protein Arginine Methyl Transferase 1 (PRMT1) is deemed to be a potential oncogenic protein considering its overexpression in several malignancies including colorectal cancer. However, the molecular pathogenesis regarding PRMT1 overexpression and overall poor patient survival involved in this devastating and life threatening cancer remains obscured. In our previous study, we have identified FAM98A as a novel substrate of PRMT1 and also identified its role in ovarian cancer progression. Here, we showed that the two structural homologs FAM98A and FAM98B included in a novel complex with DDX1 and C14orf166 are required for PRMT1 expression...
December 28, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28025045/a-novel-role-for-nhp6-proteins-in-histone-gene-regulation-in-saccharomyces-cerevisiae
#6
Diletta Durano, Andrea Lukacs, Francesca Di Felice, Gioacchino Micheli, Giorgio Camilloni
Maintaining a stable and balanced histone pool is of paramount importance for genome stability and fine regulation of DNA replication and transcription. This involves a complex regulatory machinery, exploiting transcription factors as well as histone chaperones, chromatin remodelers and modifiers. The functional details of this machinery are as yet unclear. Previous studies report histone decrease in mammalian and yeast HMGB family mutants. In this study we find that Nhp6 proteins, the S. cerevisiae HMGB1 homologues, control histone gene expression by affecting nucleosome stability at regulative regions of the histone clusters...
December 23, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28013149/how-charge-distribution-influences-the-function-of-membrane-active-peptides-lytic-or-cell-penetrating
#7
Long Chen, Qiang Zhang, Xiushuang Yuan, Yimeng Cao, Yanyan Yuan, Huiwei Yin, Xiufang Ding, Zhentai Zhu, Shi-Zhong Luo
Lytic and cell-penetrating peptides (CPPs) are both membrane-active peptides sharing similar physicochemical properties. Although their respective functions have been intensively investigated, the difference of intrinsic properties between these two types of peptides is rarely discussed. In this study, we designed a series of analogs of a recently discovered CPP ZXR-1 (FKIGGFIKKLWRSKLA) by varying the charge distributions both on the helical wheel projection and along the sequence. These peptides showed different functions on cell membranes, including membrane lytic (peptide Z1), cell-penetrating (peptide ZXR-1, Z2 and Z3), and inactive (peptide Z4) peptides...
December 21, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28013148/imaging-in-focus-reflected-light-imaging-techniques-and-applications
#8
Emily J Guggenheim, Iseult Lynch, Joshua Z Rappoport
Reflectance imaging is a broad term that describes the formation of images by the detection of illumination light that is back-scattered from reflective features within a sample. Reflectance imaging can be performed in a variety of different configurations, such as confocal, oblique angle illumination, structured illumination, interferometry and total internal reflectance, permitting a plethora of biomedical applications. Reflectance imaging has proven indispensable for critical investigations into the safety and understanding of biomedically and environmentally relevant nano-materials, an area of high priority and investment...
December 21, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28013147/hexim1-heterozygosity-stabilizes-atherosclerotic-plaque-and-decreased-steatosis-in-apoe-null-mice-fed-atherogenic-diet
#9
Manya Dhar-Mascareno, Inna Rozenberg, Jahangir Iqbal, M Mahmood Hussain, Daniel Beckles, Eduardo Mascareno
Hexim-1 is an inhibitor of RNA polymerase II transcription elongation. Decreased Hexim-1 expression in animal models of chronic diseases such as left ventricular hypertrophy, obesity and cancer triggered significant changes in adaptation and remodeling. The main aim of this study was to evaluate the role of Hexim1 in lipid metabolism focused in the progression of atherosclerosis and steatosis. We used the C57BL6 apolipoprotein E (ApoE null) crossed bred to C57BL6Hexim1 heterozygous mice to obtain ApoE null - Hexim1 heterozygous mice (ApoE-HT)...
December 21, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27988363/in-vitro-antiglioma-action-of-indomethacin-is-mediated-via-amp-activated-protein-kinase-mtor-complex-1-signalling-pathway
#10
Aleksandar Pantovic, Mihajlo Bosnjak, Katarina Arsikin, Milica Kosic, Milos Mandic, Biljana Ristic, Jelena Tosic, Danica Grujicic, Aleksandra Isakovic, Nikola Micic, Vladimir Trajkovic, Ljubica Harhaji-Trajkovic
We investigated the role of the intracellular energy-sensing AMP-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway in the in vitro antiglioma effect of the cyclooxygenase (COX) inhibitor indomethacin. Indomethacin was more potent than COX inhibitors diclofenac, naproxen, and ketoprofen in reducing the viability of U251 human glioma cells. Antiglioma effect of the drug was associated with p21 increase and G2M cell cycle arrest, as well as with oxidative stress, mitochondrial depolarization, caspase activation, and the induction of apoptosis...
December 14, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27979781/the-binding-of-the-bone-morphogenetic-protein-antagonist-gremlin-to-kidney-heparan-sulfate-such-binding-is-not-essential-for-bmp-antagonism
#11
Arnold Junior Tatsinkam, Naomi Rune, Joy Smith, Jill T Norman, Barbara Mulloy, Christopher C Rider
Gremlin-1, a bone morphogenetic protein (BMP) antagonist, has essential roles in kidney and limb bone development, and is important in chronic diseases including tissue fibrosis. It also functions as an activating ligand of the vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2), and binds strongly to the sulfated polysaccharide, heparin. Here we investigated the extent to which gremlin binds to the related polysaccharide heparan sulfate (HS), which unlike heparin is widely distributed spread within tissues...
December 12, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27974233/increased-deposition-of-glycosaminoglycans-and-altered-structure-of-heparan-sulfate-in-idiopathic-pulmonary-fibrosis
#12
Gunilla Westergren-Thorsson, Ulf Hedström, Annika Nybom, Emil Tykesson, Emma Åhrman, Marie Hornfelt, Marco Maccarana, Toin H van Kuppevelt, Göran Dellgren, Marie Wildt, Xiao-Hong Zhou, Leif Eriksson, Leif Bjermer, Oskar Hallgren
Idiopathic pulmonary fibrosis (IPF) is characterized by aberrant deposition of extracellular matrix (ECM) constituents, including glycosaminoglycans (GAGs), that may play a role in remodelling processes by influencing critical mediators such as growth factors. We hypothesize that GAGs may be altered in IPF and that this contribute to create a pro-fibrotic environment. The aim of this study was therefore to examine the fine structure of heparan sulfate (HS), chondroitin/dermatan sulfate (CS/DS) and hyaluronan (HA) in lung samples from IPF patients and from control subjects...
December 11, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27956048/omental-adipocytes-enhance-the-invasiveness-of-gastric-cancer-cells-by-oleic-acid-induced-activation-of-the-pi3k-akt-signaling-pathway
#13
Fan Xiang, Ke Wu, Yulin Liu, Liang Shi, Di Wang, Gang Li, Kaixiong Tao, Guobin Wang
A considerable number of patients with advanced gastric cancer have a clear predilection for metastasis to the great omentum, an organ mainly composed of adipose tissue. However, it remains unclear why tumor cells preferentially spread to and progress in the omentum. Here, we used a two-dimensional co-culture system to simulate the crosstalk between adipocytes and gastric cancer cells and showed that after co-culture with isolated omental adipocytes, gastric cancer cells exhibited a significant increase in lipid uptake and enhanced invasiveness...
December 9, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27939754/increasing-no-level-regulates-apoptosis-and-inflammation-in-macrophages-after-2-chloroethyl-ethyl-sulphide-challenge
#14
Satish Sagar, Soumya Ranjan Parida, Silpa Sabnam, Huma Rizwan, Sweta Pal, Mitali Madhusmita Swain, Arttatrana Pal
Generation of nitric oxide (NO) in cellular compartments acts in a redox-dependent manner to counteract oxidative stress either by directly acting as an antioxidant through scavenging superoxide anions (O2(-)), to form peroxynitrite (ONOO-) or acting as a signaling molecule, altering gene expression that triggers various physiological processes. However, the molecular mechanisms of macrophage activation and NO production leads to apoptosis and inflammation after 2-chloroethyl ethyl sulphide (CEES) exposure remains unclear...
December 9, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27939812/bis-monoacylglycero-phosphate-inhibits-tlr4-dependent-rantes-production-in-macrophages
#15
Anna Ciesielska, Hanna Sas-Nowosielska, Katarzyna Kwiatkowska
Toll-like receptor 4 (TLR4) is the receptor for bacterial lipopolysaccharide (LPS) triggering production of pro-inflammatory cytokines which help eradicate the bacteria but could also be harmful when overproduced. The signaling activity of TLR4 is modulated by cholesterol level in cellular membranes, which in turn is affected by bis(monoacylglycero)phosphate (BMP), a phospholipid enriched in late endosomes. We found that exogenously added BMP isomers become incorporated into the plasma membrane and intracellular vesicles of macrophages and strongly reduced LPS-stimulated production of a chemokine RANTES, which was correlated with inhibition of interferon regulatory factor 3 (IRF3) controlling Rantes expression...
December 7, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27923747/ibulocydine-sensitizes-human-hepatocellular-carcinoma-cells-to-trail-induced-apoptosis-via-calpain-mediated-bax-cleavage
#16
Seok Soon Park, Eunjin Jwa, Seol Hwa Shin, Eun Jin Ju, Intae Park, Jhang Ho Pak, Jung Jin Hwang, Dong-Hyung Cho, B Moon Kim, Sung-Bae Kim, Jung Shin Lee, Si Yeol Song, Seong-Yun Jeong, Eun Kyung Choi
Tumor necrosis factor-related apoptosis-induced ligand (TRAIL) induces apoptosis selectively in cancer cells without affecting the majority of normal human cells. However, hepatocellular carcinoma (HCC) cells often display resistance to TRAIL-induced apoptosis. Ibulocydine (IB) is an isobutyrate ester pro-drug of a novel synthetic Cdk inhibitor that targets Cdk7 and Cdk9. In this study, we show that treatment with subtoxic doses of IB in combination with TRAIL displays potent cytotoxicity in TRAIL-resistant human HCC cells...
December 5, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27989964/histone-acetylation-of-glucose-induced-thioredoxin-interacting-protein-gene-expression-in-pancreatic-islets
#17
Pradeep Bompada, David Atac, Cheng Luan, Robin Andersson, Judit Domènech Omella, Emilia Ottosson Laakso, Jason Wright, Leif Groop, Yang De Marinis
Thioredoxin-interacting protein (TXNIP) has been shown to be associated with glucose-induced deterioration of pancreatic beta cell function in diabetes. However, whether epigenetic mechanisms contribute to the regulation of TXNIP gene expression by glucose is not clear. Here we studied how glucose exerts its effect on TXNIP gene expression via modulation of histone acetylation marks. To achieve this, we applied clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) to knock out histone acetyltransferase (HAT) p300 in a rat pancreatic beta cell line INS1 832/13...
October 29, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27989963/tuning-constitutive-and-pathological-inflammation-in-the-gut-via-the-interaction-of-dietary-nitrate-and-polyphenols-with-host-microbiome
#18
Bárbara Rocha, Carla Nunes, João Laranjinha
Chronic inflammation is currently recognized as a critical process in modern-era epidemics such as diabetes, obesity and neurodegeneration. However, little attention is paid to the constitutive inflammatory pathways that operate in the gut and that are mandatory for local welfare and the prevention of such multi-organic diseases. Hence, the digestive system, while posing as a barrier between the external environment and the host, is crucial for the balance between constitutive and pathological inflammatory events...
October 28, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27989962/cryptic-epitopes-and-functional-diversity-in-extracellular-proteins
#19
REVIEW
Gysell M Mortimer, Rodney F Minchin
The functional diversity of proteins is a major factor determining the complexity of cells and tissues. Both translational and post-translational modifications contribute to this diversity. Recently, protein unfolding and refolding has been recognised as another mechanism for diversity by unmasking buried or cryptic sequences (epitopes) that possess physiological functions. In the current review, we focus on extracellular proteins where folding dynamics can be influenced by mechanical forces, protein-protein interactions and denaturation...
October 27, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27989965/st-john-s-wort-extract-and-hyperforin-inhibit-multiple-phosphorylation-steps-of-cytokine-signaling-and-prevent-inflammatory-and-apoptotic-gene-induction-in-pancreatic-%C3%AE-cells
#20
Michela Novelli, Marta Menegazzi, Pascale Beffy, Svetlana Porozov, Alex Gregorelli, Daniela Giacopelli, Vincenzo De Tata, Pellegrino Masiello
The extract of the herbaceous plant St. John's wort (SJW) and its phloroglucinol component hyperforin (HPF) were previously shown to inhibit cytokine-induced STAT-1 and NF-κB activation and prevent damage in pancreatic β cells. To further clarify the mechanisms underlying their protective effects, we evaluated the phosphorylation state of various factors of cytokine signaling pathways and the expression of target genes involved in β-cell function, inflammatory response and apoptosis induction. In the INS-1E β-cell line, exposed to a cytokine mixture with/without SJW extract (2-5μg/ml) or HPF (1-5μM), protein phosphorylation was assessed by Western blotting and expression of target genes by real-time quantitative PCR...
October 22, 2016: International Journal of Biochemistry & Cell Biology
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