Biochemical and Biophysical Research Communications

Published by Elsevier BV

Online ISSN: 1090-2104


Print ISSN: 0006-291X


Evidence of P-body-like structures in
  • Article

May 2007


119 Reads


Alejandro Correa





Gene expression in trypanosomatids is mainly regulated post-transcriptionally. One of the mechanisms involves the differential stability of mRNAs. However, the existence of other mechanisms involving the accessibility of mRNAs to the translation machinery cannot be ruled out. Defined cytoplasmic foci containing non-translating mRNPs, known as P-bodies, have been discovered in recent years. P-bodies are sites where mRNA can be decapped and 5'-3' degraded or stored for subsequent return to polysomes. The highly conserved DEAD box helicase Dhh1p is a marker protein of P-body functions. Here, we report the identification and cloning of a Trypanosoma cruzi Dhh1 homolog gene. TcDhh1 expression is not regulated through the parasite life cycle or under stress conditions. We show that TcDhh1 is present in polysome-independent complexes and is localized to discrete cytoplasmic foci, resembling P-bodies; these foci vary in number according to nutritional stress conditions and cycloheximide/puromycin treatment.

The Power of Methods.
  • Literature Review
  • Full-text available

September 2013


192 Reads

Major advances in science are usually launched by new methods or techniques. Because this essay is not intended as a history of science, I shall not invoke the invention of the microscope or telescope as the gateways to inner and outer space, but will restrict myself to developments I have witnessed, or almost witnessed, during my scientific lifetime.

Changes in gene expression induced by H

August 2003


65 Reads

Oxidative stress induces cardiac myocyte apoptosis. At least some effects are probably mediated through changes in gene expression. Using Affymetrix arrays, we examined the changes in gene expression induced by H(2)O(2) (0.04, 0.1, and 0.2mM; 2 and 4h) in rat neonatal ventricular myocytes. Changes in selected upregulated genes were confirmed by ratiometric RT-PCR. p21(Cip1/Waf1) was one of the only two genes upregulated in all conditions studied. Of the heat shock proteins, only Hsp70/70.1 was induced by H(2)O(2) with no change in the expression of Hsp25, Hsp60 or Hsp90. Heme oxygenase 1 was also potently upregulated, but not heme oxygenases 2 or 3. Of the intercellular adhesion proteins, syndecan-1 was significantly upregulated in response to H(2)O(2), with little change in the expression of other syndecans and no change in expression of any of the integrins studied. Thus, oxidative stress, exemplified by H(2)O(2), selectively promotes the expression of specific gene family members.

Evidence for negative feedback control of cholesterogenesis from mevalonate in liver: Absence in the intestine of guinea pigs fed A 0,5 % cholesterol diet

November 1982


20 Reads

The in vitro rate of incorporation of [2-14C]-acetate and [2-14C]-mevalonate into cholesterol of liver, ileum and caecum was determined in guinea pigs. In control animals, contrary to the situation observed when acetate was used as precursor, the rate of conversion of mevalonate to cholesterol was higher in liver than in intestine. In this latter tissue, the cholesterogenesis varied depending on the portion tested. The distribution of radiolabel derived from mevalonate between esterified and unesterified cholesterol differed among the various tissues. In cholesterol-fed guinea pigs, the plasma, liver, intestine and aorta cholesterol contents increased significantly. In addition, a negative feedback control existed for hepatic cholesterol synthesis for mevalonate and acetate. This control was absent in intestinal tissues.

A mutational analysis of DNA mimicry by Ocr, the gene 0.3 antirestriction protein of bacteriophage T7

December 2008


61 Reads

The ocr protein of bacteriophage T7 is a structural and electrostatic mimic of approximately 24 base pairs of double-stranded B-form DNA. As such, it inhibits all Type I restriction and modification (R/M) enzymes by blocking their DNA binding grooves and inactivates them. This allows the infection of the bacterial cell by T7 to proceed unhindered by the action of the R/M defence system. We have mutated aspartate and glutamate residues on the surface of ocr to investigate their contribution to the tight binding between the EcoKI Type I R/M enzyme and ocr. Contrary to expectations, all of the single and double site mutations of ocr constructed were active as anti-R/M proteins in vivo and in vitro indicating that the mimicry of DNA by ocr is very resistant to change.

Stable hyper-production of Escherichia coli beta-lactamase by Bacillus subtilis grown on a 0.5 M succinate-medium using a B. subtilis alpha-amylase secretion vector

May 1985


23 Reads

Extracellular production of Escherichia coli beta-lactamase by Bacillus subtilis, using a B. subtilis secretion vector constructed from its own alpha-amylase gene, was promoted when the cells were grown on LG-medium containing 0.5 M succinate under poor aeration conditions. The amount of the enzyme secreted was 50 to 60 times as large as that obtained by cultivation of the cells on LG-medium under good aeration conditions. The effect of protease-deficient mutant of B. subtilis on the enzyme production by B. subtilis was significant while that of protease inhibitors was negligible or inexistent.

The stimulation of light chain immunoglobulin synthesis in vitro by 0.5M salt wash of MPC-11 membrane-bound polysomes isolated in the G1 and G2 phases of the cell cycle

January 1975


13 Reads

In vitro polypeptide synthesis using a combination of G1 membrane-bound polysomes and either G1 or G2 0.5M salt wash gave appreciable incorporation into light chain immunoglobulin. When G2 polysomes were used with G2 salt wash, light chain synthesis was much reduced, however, when G2 salt wash was replaced by that from G1 then the synthesis of light chain by G2 polysomes was stimulated. The results suggest that some factor present in the G1 phase was able to activate translation of light chain mRNA which is apparently quiescent in the G2 phase.

Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution

November 2006


67 Reads

Rubredoxin (D.g. Rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas. The protein is generally purified from anaerobic bacteria in which it is thought to be involved in electron transfer or exchange processes. Rd transfers an electron to oxygen to form water as part of a unique electron transfer chain, composed by NADH:rubredoxin oxidoreductase (NRO), rubredoxin and rubredoxin:oxygen oxidoreductase (ROO) in D.g. The crystal structure of D.g. Rd has been determined by means of both a Fe single-wavelength anomalous dispersion (SAD) signal and the direct method, and refined to an ultra-high 0.68 A resolution, using X-ray from a synchrotron. Rd contains one iron atom bound in a tetrahedral coordination by the sulfur atoms of four cysteinyl residues. Hydrophobic and pi-pi interactions maintain the internal Rd folding. Multiple conformations of the iron-sulfur cluster and amino acid residues are observed and indicate its unique mechanism of electron transfer. Several hydrogen bonds, including N-H...SG of the iron-sulfur, are revealed clearly in maps of electron density. Abundant waters bound to C-O peptides of residues Val8, Cys9, Gly10, Ala38, and Gly43, which may be involved in electron transfer. This ultrahigh-resolution structure allows us to study in great detail the relationship between structure and function of rubredoxin, such as salt bridges, hydrogen bonds, water structures, cysteine ligands, iron-sulfur cluster, and distributions of electron density among activity sites. For the first time, this information will provide a clear role for this protein in a strict anaerobic bacterium.

Preparation and X-ray crystallographic analysis of rubredoxin crystals from Desulfovibrio gigas to beyond ultra-high 0.68Å resolution

October 2003


33 Reads

Rubredoxin (D.g. Rd), a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas, has been crystallized using the hanging-drop vapor diffusion method and macroseeding method. Rubredoxin crystals diffract to an ultra-high resolution 0.68 A using synchrotron radiation X-ray, and belong to the space group P2(1) with unit-cell parameters a=19.44 A, b=41.24 A, c=24.10 A, and beta=108.46 degrees. The data set of single-wavelength anomalous dispersion signal of iron in the native crystal was also collected for ab initio structure re-determination. Preliminary analysis indicates that there is one monomer with a [Fe-4S] cluster in each asymmetric unit. The crystal structure at this ultra-high resolution will reveal the details of its biological function. The crystal character and data collection strategy for ultra-high resolution will also be discussed.

Induction of stress proteins and MMP-9 by 0.8 ppm of ozone in murine skin

July 2003


88 Reads

Ozone (O(3)) is among the most reactive environmental oxidant pollutants to which cutaneous tissues are exposed. O(3) exposure has been shown to induce antioxidant depletion as well as the oxidation of lipids and proteins within the outermost skin layer, the stratum corneum. However, relatively little is known regarding the potential effects of O(3) on the cellular constituents of the underlying skin epidermis and dermis. In the present study, hairless mice exposed for 6 h to 0.8 ppm O(3) showed increases in lipid peroxidation, as quantitated by increases in 4-hydroxynonenal-protein adducts. O(3) exposure caused an induction of the stress proteins HSP27 and heme oxygenase-1 (HO-1), starting at 6 h and increasing up to 18 h after O(3) exposure. This was accompanied by an increase in matrix metalloproteinase-9 (MMP-9) mRNA and activity levels, indicative of possible injurious-reparative processes. Collectively, our data demonstrate that skin exposure to O(3) not only affects antioxidant levels and oxidation markers in the outermost stratum corneum layer, but also induces cellular stress responses in the deeper cellular layers of the skin.

Magnetic fields at extremely low-frequency (50Hz, 0.8mT) can induce the uptake of intracellular calcium levels in osteoblasts

June 2010


169 Reads

Several studies have been undertaken to elucidate the effects of electromagnetic field (EMF) on intracellular calcium ([Ca(2+)](i)) in the past 20 years. However, still there were controversies of electromagnetic pollution within the scientific community. In this work, we studied the effects of alternative magnetic fields on intracellular calcium. Osteoblastic cells were used as a model both to test the hypothesis that extremely low-frequency (ELF) magnetic fields can alter the concentrations of the intracellular calcium, and to examine the 'window' effect predicted by our previous theoretical work. The outcome of this experiment demonstrated that 50 Hz, 0.8 mT magnetic field can induce the uptake of [Ca(2+)](i) in osteoblasts. The empirical evidences of the specified window effects of [Ca(2+)](i) in osteoblastic cells were reported for the first time in this work.

Characterization and N-terminal sequence of a degradation product of 14 000 molecular weight isolated from human pancreatic juice

January 1985


9 Reads

Chromatography of human pancreatic juice has allowed the isolation of an inactive protein of 14,000 Mr (protein X) and the determination of its amino acid composition and N-terminal sequence. Protein X was found to be immunologically identical to the protein extracted from precipitates present in the pancreatic juices of patients with chronic calcifying pancreatitis and recently shown to be a degradation product of trypsinogen 1. The same chromatography performed in the presence of lima bean trypsin inhibitor has permitted the isolation of precursors of approximately congruent to 19,000 Mr which can be transformed into protein X "in vitro" by chymotrypsin hydrolysis. These results emphasize the easy activation of human pancreatic zymogens and the possible consequences due to proteolysis in pancreatic disease.

Epidermal growth factor-stimulated phosphorylation of tyrosine residues on a 120 000 dalton protein in mouse liver plasma membrane subfractions

October 1981


9 Reads

The addition of Epidermal growth factor (EGF) to mouse liver sinusoidal plasma membrane subfractions, isolated from the blood face of hepatocytes, resulted in a two to threefold increase of 32P incorporation from [γ-32P ]ATP into a 120 000 dalton protein component. The EGF-stimulation of the phosphorylation of this component was also evidenced in plasma membranes derived from the lateral and biliary faces of hepatocytes. A major phosphoamino acid residue after EGF stimulation was identified as tyrosine. An EGF-enhancement of the phosphorylation of threonine and serine residues also appears to be detectable.

Isolation of a 50 000 dalton cAMP binding protein and its characterization as a regulatory subunit of protein kinase II

March 1982


11 Reads

An unusual cAMP binding protein of 50 000 Da previously found in human tumors was isolated from HeLa cells in the presence of protease inhibitors. The protein was neutralized by anti-bovine RII antibodies but not by anti-RI. It was able to form a dimer, and to inhibit HeLa C kinase in a dose-dependent manner. The HeLa RII 50 000 was also subject to limited proteolysis and it could be phosphorylated by C kinase. HeLa cells contain two RI proteins, a predominant 49 000 Da and a minor 51 000 Da isoprotein. In addition, large amounts of a protein consisting of 19 000 and 20 000 Da subunits were isolated by 8-thio-CAMP affinity chromatography that was not immunologically related to the R proteins.

A 25 000 dalton inhibitor of cAMP independent protein kinases present in rat liver HMG protein preparations

August 1985


10 Reads

A protein kinase inhibitor was found in rat liver cells as a component of HMG proteins. It is located in cytosol as well as in nuclei. It inhibits all tested cAMP independent protein kinases and has no effect on cAMP dependent protein kinases. This inhibitor is a 25 000 Da protein. It has no ATPase, phosphoprotein phosphatase or proteinase activity and is heat unstable.

Adsorption mechanism of BMP-7 on hydroxyapatite (001) surfaces

October 2007


122 Reads

Many properties and functions of bone-related proteins perform through the interface with the hydroxyapatite. However, the mechanism of difference of proteins adsorbing behaviors caused by the variation of calcium and phosphate ions on hydroxyapatite is still unclear at atomic level. In this work, we investigated the site-selective adhesion and the adsorption mechanism of protein BMP-7 to the hydroxyapatite surfaces in aqueous media during adsorption and desorption processes. Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations combined with trajectory analysis were employed to give insight into the underlying behaviors of BMP-7 binding. The results suggest that the adsorption sites could be divided into two categories: COO(-) and NH(2)/NH3+. For COO(-), the adsorption phenomenon is driven by the electrostatic interaction formed between the negative charged carboxylate groups and the Ca1 cations on the hydroxyapatite surface. While for NH(2)/NH3+, the interaction is through the intermolecular H-bonds between the N-containing groups and the phosphate on the hydroxyapatite surface.

Imidazoline NNC77-0074 stimulates Ca2+-evoked exocytosis in INS-1E cells by a phospholipase A2-dependent mechanism

May 2003


25 Reads

We have previously demonstrated that the novel imidazoline compound (+)-2-(2-(4,5-dihydro-1H-imidazol-2-yl)-thiopene-2-yl-ethyl)-pyridine (NNC77-0074) increases insulin secretion from pancreatic beta-cells by stimulation of Ca(2+)-dependent exocytosis. Using capacitance measurements, we now show that NNC77-0074 stimulates exocytosis in clonal INS-1E cells. NNC77-0074-stimulated exocytosis was antagonised by the cytoplasmic phospholipase A(2) (cPLA(2)) inhibitors ACA and AACOCF(3) and in cells treated with antisense oligonucleotide against cPLA(2)alpha. NNC77-0074-evoked insulin secretion was likewise inhibited by ACA, AACOCF(3), and cPLA(2)alpha antisense oligonucleotide treatment. In pancreatic islets NNC77-0074 stimulated PLA(2) activity. We propose that cPLA(2)alpha plays an important role in the regulation of NNC77-0074-evoked exocytosis in insulin secreting beta-cells.

Yamagishi S, Inagaki Y, Amano S, Okamoto T, Takeuchi M & Makita Z. Pigment epithelium-derived factor protects cultured retinal pericytes from advanced glycation end product-induced injury through its antioxidative properties. Biochem Biophys Res Commun296: 877-882 10.1016/S0006-291X(02)00940-3

September 2002


71 Reads

Pigment epithelium-derived factor (PEDF) has recently been shown to be the most potent inhibitor of angiogenesis in the mammalian eye, suggesting that loss of PEDF is involved in the pathogenesis of proliferative diabetic retinopathy. However, a protective role for PEDF in pericyte loss in early diabetic retinopathy remains to be elucidated. In this study, we investigated whether PEDF proteins could protect against advanced glycation end product (AGE)-induced injury in retinal pericytes. Ligand blot analysis revealed that pericytes possessed a membrane protein with binding affinity for PEDF. PEDF proteins were found to significantly inhibit AGE-induced reactive oxygen species (ROS) generation and the subsequent decrease in DNA synthesis and apoptotic cell death in pericytes. Further, PEDF proteins completely restored the down-regulation of bcl-2 gene expression in AGE-exposed pericytes. The results demonstrated that PEDF proteins protected cultured pericytes from AGE-induced cytotoxicity through its anti-oxidative properties. Our present study suggests that substitution of PEDF proteins may be a promising strategy in treatment of patients with early diabetic retinopathy.

Crystal structure of a thermostable Old Yellow Enzyme from Thermus scotoductus SA-01

February 2010


297 Reads

Recent characterization of the chromate reductase (CrS) from the thermophile Thermus scotoductus SA-01 revealed this enzyme to be related to the Old Yellow Enzyme (OYE) family. Here, we report the structure of a thermostable OYE homolog in its holoform at 2.2A as well as its complex with p-hydroxybenzaldehyde (pHBA). The enzyme crystallized as octamers with the monomers showing a classical TIM barrel fold which upon dimerization yields the biologically active form of the protein. A sulfate ion is bound above the si-side of the non-covalently bound FMN cofactor in the oxidized solved structure but is displaced upon pHBA binding. The active-site architecture is highly conserved as with other members of this enzyme family. The pHBA in the CrS complex is positioned by hydrogen bonding to the two conserved catalytic-site histidines. The most prominent structural difference between CrS and other OYE homologs is the size of the "capping domain". Thermostabilization of the enzyme is achieved in part through increased proline content within loops and turns as well as increased intersubunit interactions through hydrogen bonding and complex salt bridge networks. CrS is able to reduce the C=C bonds of alpha,beta-unsaturated carbonyl compounds with a preference towards cyclic substrates however no activity was observed towards beta-substituted substrates. Mutational studies have confirmed the role of Tyr177 as the proposed proton donor although reduction could still occur at a reduced rate when this residue was mutated to phenylalanine.

Expression and Regulation by Insulin of Glut 3 in UMR 106-01, a Clonal Rat Osteosarcoma Cell Line

February 1996


18 Reads

Expression of the glucose transporter GLUT 3 is mainly restricted to neuronal tissues, with lower levels in testis and placenta. In addition, GLUT 3 has recently been reported in neonatal rat calvaria by in situ hybridisation. We report the co-expression of GLUT 1 and GLUT 3 mRNA and protein in UMR 106-01, a clonal osteosarcoma cell line. By semi-quantitative analysis we show that GLUT 3 protein is expressed at levels comparable to GLUT 1. Insulin stimulates glucose uptake in UMR 106-01 cells. GLUT 3 mRNA and protein are increased by chronic (16 h) treatment with insulin, and the increase in GLUT 3 mRNA is not inhibited by cycloheximide. Regulation of GLUT 3 mRNA by insulin has not been previously shown. UMR 106-01 represents a useful model for investigating regulation of GLUT 3 expression.

Identification of the genomic region determining serotype specificity of Vibrio cholerae 01

April 1991


13 Reads

A 2.1-kb genomic region responsible for Ogawa serotype specificity of Vibrio cholerae 01 was identified by cosmid cloning and recombinant plasmid experiments. The plasmid carrying this region derived from Ogawa type Vibrio cholerae NIH 41 coded for a specific protein of 27 kD, and was found to convert serotype specificity from Inaba to Ogawa when co-introduced into the Escherichia coli cells harboring a cloned 20-kilobase genomic DNA fragment of Inaba type Vibrio cholerae 35A3.

Thrombin-induced calcium oscillation in human platelets and MEG-01, a megakaryoblastic leukemia cell line

April 1992


12 Reads

Digital imaging microscopy revealed that human platelets show periodic intracellular Ca++ elevation in response to 0.01 U/ml thrombin. MEG-01, a megakaryoblastic leukemia cell line, also responded with oscillatory intracellular Ca++ elevation (0.7-1 times/min) to thrombin (0.001-0.003U/ml). Ca++ transients appears to be fused with higher thrombin doses. With extracellular Ca++ concentrations of 0.1 mM or less, Ca++ oscillation could not be elicited, or even when present, it disappeared after a few spikings of [Ca++]i. Extracellular Ca++ concentrations of 0.3 mM or more were required to facilitate ongoing Ca++ oscillation, suggesting an important role of Ca++ influx for Ca++ oscillation.

SL-01, an oral derivative of gemcitabine, inhibited human breast cancer growth through induction of apoptosis

July 2013


34 Reads

Unlabelled: SL-01 is an oral derivative of gemcitabine that was synthesized by introducing the moiety of 3-(dodecyloxycarbonyl) pyrazine-2-carbonyl at N4-position on cytidine ring of gemcitabine. We aimed to evaluate the efficacy of SL-01 on human breast cancer growth. SL-01 significantly inhibited MCF-7 proliferation as estimated by colorimetric assay. Flow cytometry assay indicated the apoptotic induction and cell cycle arrest in G1 phase. SL-01 modulated the expressions of p-ATM, p53 and p21 and decrease of cyclin D1 in MCF-7 cells. Further experiments were performed in a MCF-7 xenografts mouse model. SL-01 by oral administration strongly inhibited MCF-7 xenografts growth. This effect of SL-01 might arise from its roles in the induction of apoptosis. Immunohistochemistry assay showed the increase of TUNEL staining cells. Western blotting indicated the modulation of apoptotic proteins in SL-01-treated xenografts. During the course of study, there was no evidence of toxicity to mice. In contrast, the decrease of neutrophil cells in peripheral and increase of AST and ALT levels in serum were observed in the gemcitabine-treated mice. Conclusion: SL-01 possessed similar activity against human breast cancer growth with gemcitabine, whereas, with lower toxicity to gemcitabine. SL-01 is a potent oral agent that may supplant the use of gemcitabine.

UCN-01, 7-Hydroxyl-staurosporine, Inhibits Kinase Activity of Cyclin-Dependent Kinases and Reduces the Phosphorylation of the Retinoblastoma Susceptibility Gene Product in A549 Human Lung Cancer Cell Line

March 1996


42 Reads

UCN-01 (7-hydroxyl-staurosporine), which was initially developed as a selective protein kinase C inhibitor, has an anti-tumor effect on several human cancer cell lines in vivo. In this study, we examined whether this compound has an inhibitory effect on cell cyclin-dependent kinases (cdks) in vitro and in vivo using A549 human lung adenocarcinoma cell line. UCN-01 inhibited the retinoblastoma susceptibility gene product (pRB) kinase activity of three types of cdks (cdk 2, 4 and 6) with 50% inhibitory concentration values of 42, 32, and 58 nM, respectively, in vitro. Moreover, the amount of phosphorylated pRB was reduced by UCN-01 at a concentration of 100 nM in the living cells. Flow cytometric analysis showed that UCN-01 inhibited cell cycle progression at G1 to S transition in A549 cells at the concentration of 100 nM. These results suggest that inhibition of pRB phosphorylation by UCN-01 might lead to inhibition of the cell cycle and thereby contribute to antitumor activity of this compound.

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