Carbamylation of proteins in 2-D electrophoresis--myth or reality?

Carbamylation is widely quoted as being a problem in 2-D gel analysis and the associated sample preparation steps. This modification occurs when iso-cyanate, a urea break-down product, covalently modifies lysine residues, thus inducing a change in isoelectric point. Urea is used at up to 9 M concentrations in sample preparation and 2-D gels because of its ability to disrupt protein structure and effect denaturation without the need for ionic surfactants such as SDS. We have studied carbamylation using 7 M urea and 2 M thiourea, under a range of experimental temperatures to establish when, and if, it occurs and what can be done to minimize the modification. The actual time required for protein extraction from a tissue is usually short compared to the time required for procedures such as reduction and alkylation and IPG rehydration and focusing. Therefore, it is the temperature during these post-extraction procedures that is the most critical factor. Our experiments have shown that carbamylation does not occur during electrophoresis in the presence of urea, even with prolonged run-times. However, under poorly controlled sample preparation and storage conditions, it can become a major event.     

Home alone? Effect of weather-induced behaviour on spread of SARS-CoV-2 in Germany

In early 2020 the world was struck by the epidemic of novel SARS-CoV-2 virus. Like many others, German government has introduced severe contact restrictions to limit the spread of infection. This paper analyses effects of weather on the spread of the disease under the described circumstances. We demonstrate that regions reported lower growth rates of the number of the infection cases after days with higher temperatures, no rain and low humidity. We argue that this effect is channelled through human behaviour. The evidence suggests that “good” weather attracts individuals to outdoor (safer) environments, thus, deterring people from indoor (less safe) environments. Understanding this relationship is important for improving the measures aiming at combating the spread of the virus.     

Cox-2: Where are we in 2003? - The role of cyclooxygenase-2 in bone repair

Prostaglandins are important mediators of bone repair, and cyclooxygenases are required for prostaglandin production. Data from animal studies suggest that both non-specific and specific inhibitors of cyclooxygenases impair fracture healing but that this is due to the inhibition of COX-2 and not COX-1. Although these data raise concerns about the use of COX-2-specific inhibitors as anti-inflammatory or anti-analgesic drugs in patients undergoing bone repair, clinical reports have been inconclusive. Because animal data suggest that the effects of COX-2 inhibitors are both dose-dependent and reversible, in the absence of scientifically sound clinical evidence it is suggested that physicians consider short-term administration or other drugs in the management of these patients.     

Involvement of the TPR2 subdomain movement in the activities of ?29 DNA polymerase

The polymerization domain of ϕ29 DNA polymerase acquires a toroidal shape by means of an arch-like structure formed by the specific insertion TPR2 (Terminal Protein Region 2) and the thumb subdomain. TPR2 is connected to the fingers and palm subdomains through flexible regions, suggesting that it can undergo conformational changes. To examine whether such changes take place, we have constructed a ϕ29 DNA polymerase mutant able to form a disulfide bond between the apexes of TPR2 and thumb to limit the mobility of TPR2. Biochemical analysis of the mutant led us to conclude that TPR2 moves away from the thumb to allow the DNA polymerase to replicate circular ssDNA. Despite the fact that no TPR2 motion is needed to allow the polymerase to use the terminal protein (TP) as primer during the initiation of ϕ29 TP–DNA replication, the disulfide bond prevents the DNA polymerase from entering the elongation phase, suggesting that TPR2 movements are necessary to allow the TP priming domain to move out from the polymerase during transition from initiation to elongation. Furthermore, the TPR2-thumb bond does not affect the equilibrium between the polymerization and exonuclease activities, leading us to propose a primer-terminus transference model between both active sites.     

Is 2-phosphoglycerate-dependent automodification of bacterial enolases implicated in their export?

We observed that in vivo and in vitro a small fraction of the glycolytic enzyme enolase became covalently modified by its substrate 2-phosphoglycerate (2-PG). In modified Escherichia coli enolase, 2-PG was bound to Lys341, which is located in the active site. An identical reversible modification was observed with other bacterial enolases, but also with enolase from Saccharomyces cerevisiae and rabbit muscle. An equivalent of Lys341, which plays an important role in catalysis, is present in enolase of all organisms. Covalent binding of 2-PG to this amino acid rendered the enzyme inactive. Replacement of Lys341 of E.coli enolase with other amino acids prevented the automodification and in most cases strongly reduced the activity. As reported for other bacteria, a significant fraction of E.coli enolase was found to be exported into the medium. Interestingly, all Lys341 substitutions prevented not only the automodification, but also the export of enolase. The K341E mutant enolase was almost as active as the wild-type enzyme and therefore allowed us to establish that the loss of enolase export correlates with the loss of modification and not the loss of glycolytic activity.     

Propagation of electromagnetic radiation in mitochondria?

Infanticide by primate males was considered rare if groups contain more than one adult male because, owing to lower paternity certainty, a male should be less likely to benefit from infanticide. Guided by recent evidence for strong variation of infanticide in primate multi-male groups, we modelled the conditions for when infanticide should occur for a group with a resident and an immigrant male. Setting the parameters (e.g. infant mortality, reduction of interbirth interval, life-time reproductive success, genetic representation) to fit the conditions most commonly found in nature, we develop a game-theoretic model to explore the influence of age and dominance on the occurrence of infanticide and infant defence. Male age strongly impacts the likelihood of an attack which is modified by the father's defence. If the new male is dominant he is likely to attack under most circumstances whereas a subordinate male will only attack if the father does not defend. These model scenarios fit the conditions under which infanticide is known to occur in primate multi-male groups and offer an explanation why infanticide is common in some multi-male groups and rare in others. Overall, the benefits for infanticidal males are strongly governed by a reduced interbirth interval while advantages via improved genetic representation in the gene pool contribute but a minor fraction.     

Is adrenomedullin a causal agent in some cases of type 2 diabetes?

The study of two populations with a recent onset of type 2 diabetes showed that a subset of the patients had higher levels of adrenomedullin (AM) than the rest of the diabetics. In this subset, physiological elevations of AM might have triggered the disease in predisposed individuals. Diabetics showed higher levels of AM than healthy controls. In addition, glycemia was measured in diabetic rats after injection of saline, AM, or antiAM antibody. AM elevated glycemia, whereas the antibody reduced circulating glucose to normal. These results suggest that manipulation of AM levels could represent a new approach in the management of diabetes for the appropriate individuals.     

A role of PPARgamma in reproduction?

Synthetic molecules of the glitazone family are currently used in the treatment of type II diabetes. Glitazones also improve secondary pathologies that are frequently associated with insulin resistance such as the polycystic ovary syndrome (PCOS). Glitazones bind to the peroxysome proliferator-activated receptor gamma (PPARgamma), a nuclear receptor which is highly expressed in adipose tissue. PPARgamma also binds natural ligands such as long-chain fatty acids. Recently, several groups have shown that PPARgamma is also highly expressed in ovarian granulosa cells, and that glitazones are able to modulate in vitro granulosa cell proliferation and steroidogenesis in several species. These recent data raise new questions concerning the underlying mechanism of the effect of glitazones on PCOS. One might hypothesize, as for other < glucophage > molecules such as metformin, that it is the general improvement of glucose metabolism and insulin sensitivity by glitazones which indirectly, and via an unknown mechanism, ameliorates ovarian functionality. The data discussed here suggest now an alternative possibility, that glitazones act directly at the ovarian level. Moreover, PPARgamma also seems to play a key role in the maturation of the placenta. In particular, inactivation of PPARgamma in mice is lethal, since the foetus is unable to develop because of alterations of placental maturation. In women, the activation of PPARgamma in placenta leads to an increase of placental hormone secretion. Overall, these results raise some questions about the role of natural ligands of PPARgamma such as long chain fatty acids on female fertility and the interactions between energy metabolism and reproduction in general.     

Does GABA increase the efficiency of symbiotic N2 fixation in legumes?

The ability to regulate the rates of metabolic processes in response to changes in the internal and/or external environment is a fundamental feature which is inherent in all organisms. This adaptability is necessary for conserving the stability of the intercellular environment (homeostasis) which is essential for maintaining an efficient functional state in the organism. Symbiotic nitrogen fixation in legumes is an important process which establishes from the complex interaction between the host plant and microorganism. This process is widely believed to be regulated by the host plant nitrogen demand through a whole plant N feedback mechanism in particular under unfavorable conditions. This mechanism is probably triggered by the impact of shoot-borne, phloem-delivered substances. The precise mechanism of the potential signal is under debate, however, the whole phenomenon is probably related to a constant amino acid cycling within the plant, thereby signaling the shoot nitrogen status. Recent work indicating that there may be a flow of nitrogen to bacteroids is discussed in light of hypothesis that such a flow may be important to nodule function. Large amount of γ-aminobutyric acid (GABA) are cycled through the root nodules of the symbiotic plants. In this paper some recent evidence concerning the possible role of GABA in whole-plant-based upregulation of symbiotic nitrogen fixation will be reviewed.Key words: γ-aminobutyric acid, nitrogen fixation, nodule, symbiosis, translocation, signalingNitrogen (N) is major limiting nutrient for the growth of most plant species in different ecosystems. Acquisition and assimilation of N is second in importance only to photosynthesis for plant growth and development. Elemental N is a key constituent of protein, nucleic acids and other vital cellular components. Most plants acquire N from the soil solution either as nitrate or ammonium ions. In addition, some plants can utilize the atmospheric gaseous nitrogen pool through symbiotic associations with species of bacteria, cyanobacteria or actinomycetes that contain the N₂ fixing enzyme, nitrogenase. Clearly, the crucial role that symbiotic plants play in plant growth requires that physiologists understand the biochemical and molecular events that regulate fixation and subsequent metabolism of nitrogen.Symbiotic N₂ fixation is an important process for increasing the plant available N and thereby the growth capacity of legumes. This process results from the complex interaction between the host plant and microorganism.¹ The host plant provides the microorganism with carbon and a source of energy for growth and functions while the microorganism fixes atmospheric N₂ and provides the plant with a source of reduced nitrogen in the form of ammonium. An adequate supply of carbohydrates is an essential requirement of nodule functioning as N₂ fixation is expensive in terms both of energy and carbon for the synthesis of N-products. Sucrose synthesized in photosynthesis and exported to the nodules via the phloem, is the primary fuel for N₂ fixation.² Sucrose can be metabolized in the cytoplasm of infected, uninfected or interstitial cells with organic acids as the end products. Malate is strongly believed to be the major respiratory substrate for bacteroids.³ This dicarboxylic acid is the major energy source for the bacteroids and plant mitochondria, and is used for NH₄⁺ assimilation as carbon skeleton in the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway.⁴ The products of symbiotic N₂ fixation are exported from the nodules to the rest of the host plant where they are incorporated into essential macro-molecules such as amino acids, proteins that drive plant growth, development and yields. According to the fixation products, root nodules are generally divided into two major groupings:¹ (1) indeterminate nodules that are elongate-cylindrical activity that transport fixed N as amides such as alfalfa, pea and clover; and (2) determinate nodules that are spherical with determinate internal meristematic activity that transport fixed N as ureides, such as soybean and common bean. The complex series of events leading to the formation and functioning of the fixation machinery required controlled coordinated expression of both bacterial and host plant genes.     

A role for anti-transglutaminase 2 autoantibodies in the pathogenesis of coeliac disease?

Coeliac disease is an autoimmune-mediated disorder with both innate and adaptive immune components. The disease is triggered by dietary gluten, which provokes the development of a massive immune reaction leading to the destruction of the small-intestinal mucosal morphology and intestinal dysfunction. Besides the typical small-bowel symptoms extraintestinal manifestations may also arise in a subset of coeliac disease patients. In addition, gluten evokes the production of antibodies mainly targeting deamidated gluten peptides or transglutaminase 2. Although coeliac disease has traditionally been regarded as a T cell-mediated disorder, this review discusses the role of the gluten-induced disease-specific anti-transglutaminase 2-autoantibodies in the pathogenesis of the disease.     

Effects of SGLT2 Inhibition in Human Kidney Proximal Tubular Cells—Renoprotection in Diabetic Nephropathy?

Sodium/glucose cotransporter 2 (SGLT2) inhibitors are oral hypoglycemic agents used to treat patients with diabetes mellitus. SGLT2 inhibitors block reabsorption of filtered glucose by inhibiting SGLT2, the primary glucose transporter in the proximal tubular cell (PTC), leading to glycosuria and lowering of serum glucose. We examined the renoprotective effects of the SGLT2 inhibitor empagliflozin to determine whether blocking glucose entry into the kidney PTCs reduced the inflammatory and fibrotic responses of the cell to high glucose. We used an in vitro model of human PTCs. HK2 cells (human kidney PTC line) were exposed to control 5 mM, high glucose (HG) 30 mM or the profibrotic cytokine transforming growth factor beta (TGFβ1; 0.5 ng/ml) in the presence and absence of empagliflozin for up to 72 h. SGLT1 and 2 expression and various inflammatory/fibrotic markers were assessed. A chromatin immunoprecipitation assay was used to determine the binding of phosphorylated smad3 to the promoter region of the SGLT2 gene. Our data showed that TGFβ1 but not HG increased SGLT2 expression and this occurred via phosphorylated smad3. HG induced expression of Toll-like receptor-4, increased nuclear deoxyribonucleic acid binding for nuclear factor kappa B (NF-κB) and activator protein 1, induced collagen IV expression as well as interleukin-6 secretion all of which were attenuated with empagliflozin. Empagliflozin did not reduce high mobility group box protein 1 induced NF-κB suggesting that its effect is specifically related to a reduction in glycotoxicity. SGLT1 and GLUT2 expression was not significantly altered with HG or empagliflozin. In conclusion, empagliflozin reduces HG induced inflammatory and fibrotic markers by blocking glucose transport and did not induce a compensatory increase in SGLT1/GLUT2 expression. Although HG itself does not regulate SGLT2 expression in our model, TGFβ increases SGLT2 expression through phosphorylated smad3.     

Phosphatases Involved in Modulation of Gap Junctional Intercellular Communication and Dephosphorylation of Connexin43 in Hamster Fibroblasts: 2B or Not 2B?

12-O-Tetradecanoylphorbol-13-acetate (TPA) caused strong suppression of gap junctional intercellular communication, altered phosphorylation status of the gap junction protein, connexin43, and disappearance of immunorecognizible connexin43-containing gap junction plaques in V79 fibroblasts. When TPA was removed, all parameters normalized during a 3- to 4-h period. The normalizations were independent of protein synthesis, suggesting the possible involvement of phosphatases. None of the phosphatase inhibitors okadaic acid, calyculin A, cyclosporin A, or FK506 affected intercellular communication or connexin43 phosphorylation status on their own. In sequential exposures to TPA and phosphatase inhibitors, only the protein-phosphatase 2B (PP2B) inhibitors cyclosporin A and FK506 delayed the recovery of the studied parameters. Rapamycin binds to the same set of proteins as does FK506, but without inhibiting PP2B. Rapamycin did not affect the recovery of intercellular communication, but it delayed the normalization of connexin43 band pattern and immunorecognition of gap junction plaques. Dephosphorylation of immunoprecipitated connexin43 was studied using PP1, 2A, 2B, and 2C. PP2A was the most efficient (by 100-fold on a molar basis). Connexin43 immunoprecipitated from TPA-exposed cells was a poor substrate for PP1, 2B, and 2C. Thus, PP2B appeared to play a role in normalization of intercellular communication, but not necessarily in direct dephosphorylation of connexin43. Peptidyl-prolyl isomerase activity of cyclosporin/FK506/rapamycin-binding proteins may promote the dephosphorylation of connexin43 in cells.     

Protective effect of autophagy in anoxia-reoxygenation of isolated cardiomyocyte?

Preconditioning and postconditioning increased numbers of living cells and decreased that of necrotic, apoptotic and autophagic cells in anoxia-reoxygenation of isolated cardiomyocytes. It was established that proteasome inhibitors prevented the necrotic and apoptotic cell death of cardiomyocytes in anoxia-reoxygenation and in such a way reproduce the effect of pharmacological preconditioning and postconditioning. In this case, the population of autophagic cardiomyocytes has not changed considerably or had a tendency of increasing compared to anoxia-reoxygenation. The data obtained showed that the specific protective effect of proteasome inhibitors could be caused by autophagy activation. In our recent experiments new data supporting this hypothesis were obtained. The inhibition of autophagy with N-3-methyladenine during anoxia-reoxygenation caused an increase in the number of necrotic cells and a decrease of the live cell population. Moreover, simultaneous inhibition of both autophagy and apoptosis (N-3-methyladenine and caspase-3 inhibitor application) in anoxia-reoxygenation led to a dramatic increase of necrotic cardiomyocytes and a concomitant decrease in the number of living cells. Thus, the process of autophagy in cardiomyocytes during anoxia-reoxygenation may lead not only to programmed cell death, but has also some protective effect. The mechanisms of this phenomenon are still in need of thorough investigation.     

In?Vivo Kinetics of Segregation and Polar Retention of MS2-GFP-RNA Complexes in Escherichia coli

The cytoplasm of Escherichia coli is a crowded, heterogeneous environment. From single cell live imaging, we investigated the spatial kinetics and heterogeneities of synthetic RNA-protein complexes. First, although their known tendency to accumulate at the cell poles does not appear to introduce asymmetries between older and newer cell poles within a cell lifetime, these emerge with cell divisions. This suggests strong polar retention of the complexes, which we verified in their history of positions and mean escape time from the poles. Next, we show that the polar retention relies on anisotropies in the displacement distribution in the region between midcell and poles, whereas the speed is homogeneous along the major cell axis. Afterward, we establish that these regions are at the border of the nucleoid and shift outward with cell growth, due to the nucleoid’s replication. Overall, the spatiotemporal kinetics of the complexes, which is robust to suboptimal temperatures, suggests that nucleoid occlusion is a source of dynamic heterogeneities of macromolecules in E. coli that ultimately generate phenotypic differences between sister cells.     

Does in vitro activation of postsynaptic alpha 2-adrenoceptor utilize intracellular Ca2+ for contraction in dog saphenous vein?

Dog saphenous vein spiral strips were employed to determine whether an intracellular source of Ca2+ is used for contraction upon activation of the alpha 2-adrenoceptor by B-HT 920 in Ca2+-free Krebs solution containing 50 microM EGTA. The studies were carried out in parallel with the activation of the alpha 1-adrenoceptor by phenylephrine (Phe) under the condition that B-HT 920 (10(-5) M) and Phe (2 x 10(-6) M) gave rise to a similar level of responses in Ca2+-containing Krebs solution. A similar level of responses to these agonists at equieffective concentrations in Ca2+-free medium were also observed. Such responses to Phe and B-HT 920 were inhibited by 10(-7) M rauwolscine and 10(-7) M prazosin, respectively, and were not affected by 10(-7) M nifedipine or 5 mM Mn2+. The responses to B-HT 920 (10(-5) M) and submaximal concentration of Phe (2 x 10(-6) M) in Ca2+-free medium were additive. However, if the vascular strips were first contracted maximally with 10(-4) M Phe in Ca2+-free medium to deplete the intracellular Ca store, subsequent addition of B-HT 920 failed to induce additional response. Our results strongly suggest that activation of alpha 2-adrenoceptor in dog saphenous vein in Ca2+-free medium indeed utilizes intracellular Ca2+ for contraction. We also found that the failure of earlier studies to demonstrate the contractile effects of B-HT 920 in dog saphenous vein was due to experimental artifacts derived from the use of high concentration of EGTA and artificial pH-buffering reagent.