Why do proteins use selenocysteine instead of cysteine?

Selenocysteine is present in a variety of proteins and catalyzes the oxidation of thiols to disulfides and the reduction of disulfides to thiols. Here, we compare the kinetic and thermodynamic properties of cysteine with its selenium-containing analogon, selenocysteine. Reactions of simple selenols at pH 7 are up to four orders of magnitude faster than their sulfur analogs, depending on reaction type. In redox-related proteins, the use of selenium instead of sulfur can be used to tune electrode, or redox, potentials. Selenocysteine could also have a protective effect in proteins because its one-electron oxidized product, the selanyl radical, is not oxidizing enough to modify or destroy proteins, whereas the cysteine-thiyl radical can do this very rapidly.     

Do mitochondria make nitric oxide? no?

Several papers have claimed that mitochondria contain nitric oxide synthase (NOS) and make nitric oxide (NO*) in amounts sufficient to affect mitochondrial respiration. However, we found that the addition of L-arginine or the NOS inhibitor L-NMMA to intact rat liver mitochondria did not have any effect on the respiratory rate in both State 3 and State 4. We did not detect mitochondrial NO* production by the oxymyoglobin oxidation assay, or electrochemically using an NO* electrode. An apparent NO* production detected by the Griess assay was identified as an artifact. NO* generated by eNOS added to the mitochondria could easily be detected, although succinate-supplemented mitochondria appeared to consume NO*. Our data show that NO* production by normal rat liver mitochondria cannot be detected in our laboratory, even though the levels of production claimed in the literature should easily have been measured by the techniques used. The implications for the putative mitochondrial NOS are discussed.     

Is nitric oxide luteolytic or antiluteolytic?

Nitric oxide (NO) has been reported to be luteolytic based on treatment of cows in vivo with an inhibitor of nitric oxide synthase (NOS-produces NO), which delayed the decline in progesterone by two to three days [Jaroszewki J, Hansel, W. Intraluteal administration of a nitric oxide synthase blocker stimulates progesterone, oxytocin secretion and prolongs the life span of the bovine corpus luteum. Proc Soc Exptl Biol Med 2000;224:50-5; Skarzynski D, Jaroszewki J, Bah, M, et al. Administration of nitric oxide synthase inhibitor counteracts prostaglandin F(2alpha)-induced luteolysis in cattle. Biol Reprod 2003;68:1674-81]. The objective of this experiment was to determine the effect of a long acting NO donor or a NOS inhibitor infused chronically into the interstitial tissue of the ovarian vascular pedicle adjacent to the ovary with a corpus luteum on secretion of progesterone during the ovine estrous cycle. Ewes were treated either with Vehicle (N=5); Diethylenetriamine (DETA-control for DETA-NONOate; N=5); (Z)-1-[2-(2-aminoethyl)-N-(2-ammonioethyl) amino]diazen-1-ium-1,2-diolate (DETA-NONOate-long acting NO donor; N=6); or l-nitro-arginine methyl ester (l-NAME-NOS inhibitor; N=6) every 6 h from 24:00 h (0 h) on day 8 through 18:00 h on day 18 of the estrous cycle. Jugular venous blood was collected every 6h for analysis for progesterone and corpora lutea were collected at 18:00 h on day 18 and weighed. Weights of corpora lutea were heavier (P< or =0.05) in DETA-NONOate-treated ewes when compared to Vehicle, DETA, or l-NAME-treated ewes, which did not differ amongst each other (P> or =0.05). Profiles of progesterone in jugular venous blood on days 8-18 differed (P< or =0.05) in DETA-NONOate-treated ewes when compared to Vehicle, DETA, or l-NAME-treated ewes did not differ (P> or =0.05) amongst each other. It is concluded that NO is not luteolytic during the ovine estrous cycle, but may instead be antiluteolytic and prevent luteolysis.     

Why use bubble-column bioreactors?

Among the plethora of bioreactors available for aerobic culture, bubble columns, which are composed of a cylindrical vessel fitted with a gas sparger, are gaining in use. The simple construction of bubble-column reactors makes them easy to maintain. In addition, it is possible to control the degree of shear, uniformly within the reactor, which is critical to the growth of plant and animal cells in particular. This article reviews in detail the hydrodynamic, heat and mass-transfer characteristics of bubble-column bioreactors - parameters that are important for industrial scale-up.     

Inhibition of hepatocyte lipogenesis by nitric oxide donor: could nitric oxide regulate lipid synthesis?

Tissue lipogenesis is variably controlled by substrate supply and hormones. The possibility that nitric oxide (NO) might regulate lipogenesis derives from the action of NO on coenzyme A (CoA) to produce metabolically inactive S-nitrosoCoA. The effect of the nitric oxide donor S-nitrosoglutathione (GSNO) on long chain fatty acid and cholesterol synthesis was measured in isolated cultured rat hepatocytes. [1-14C] Butyrate was used as substrate to measure 14C incorporation into lipids as butyrate is twice as effective as acetate in hepatic lipogenesis and is ketogenic via the Lynen cycle. NO very significantly (P < 0.01) impaired long chain fatty acid and cholesterol synthesis an observation dependent upon time of exposure (3 h pre-incubation or 6 h continuous exposure) and concentration of GSNO (500 microM to 2.0 mM). Decrease in hepatic lipogenesis was paralleled by decrease in ketogenesis. ATP levels remained unchanged following short-term exposure to GSNO. Exposure of hepatocytes to GSNO together with 2.0 mM glutathione significantly diminished the inhibition of lipogenesis induced by GSNO alone. Impairment of lipogenesis by GSNO appears not to be limited by energy supply and now adduced, but not proven, to be operative via the degree of inactivation of cytosolic CoA. NO control of lipogenesis could be clinically important where NO production is increased as in demyelinating diseases, chronic arthritis or colitis and in wasting diseases such as AIDS.     

Why do bacteria use so many enzymes to scavenge hydrogen peroxide?

Hydrogen peroxide (H(2)O(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. Because H(2)O(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. Mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. In order to understand how bacteria cope with oxidative stress, it is important to identify the key enzymes involved in H(2)O(2) degradation. Catalases and NADH peroxidase (Ahp) are primary scavengers in many bacteria, and their activities and physiological impacts have been unambiguously demonstrated through phenotypic analysis and through direct measurements of H(2)O(2) clearance in vivo. Yet a wide variety of additional enzymes have been proposed to serve similar roles: thiol peroxidase, bacterioferritin comigratory protein, glutathione peroxidase, cytochrome c peroxidase, and rubrerythrins. Each of these enzymes can degrade H(2)O(2) in vitro, but their contributions in vivo remain unclear. In this review we examine the genetic, genomic, regulatory, and biochemical evidence that each of these is a bonafide scavenger of H(2)O(2) in the cell. We also consider possible reasons that bacteria might require multiple enzymes to catalyze this process, including differences in substrate specificity, compartmentalization, cofactor requirements, kinetic optima, and enzyme stability. It is hoped that the resolution of these issues will lead to an understanding of stress resistance that is more accurate and perceptive.     

Why do we still use stepwise modelling in ecology and behaviour?

1. The biases and shortcomings of stepwise multiple regression are well established within the statistical literature. However, an examination of papers published in 2004 by three leading ecological and behavioural journals suggested that the use of this technique remains widespread: of 65 papers in which a multiple regression approach was used, 57% of studies used a stepwise procedure. 2. The principal drawbacks of stepwise multiple regression include bias in parameter estimation, inconsistencies among model selection algorithms, an inherent (but often overlooked) problem of multiple hypothesis testing, and an inappropriate focus or reliance on a single best model. We discuss each of these issues with examples. 3. We use a worked example of data on yellowhammer distribution collected over 4 years to highlight the pitfalls of stepwise regression. We show that stepwise regression allows models containing significant predictors to be obtained from each year's data. In spite of the significance of the selected models, they vary substantially between years and suggest patterns that are at odds with those determined by analysing the full, 4-year data set. 4. An information theoretic (IT) analysis of the yellowhammer data set illustrates why the varying outcomes of stepwise analyses arise. In particular, the IT approach identifies large numbers of competing models that could describe the data equally well, showing that no one model should be relied upon for inference.     

Why do animals hybridize?

Animal hybridization is increasingly recognized as common and evolutionarily important, but the role of behavior in promoting hybridization events is not well understood. Understanding the behavioral causes of hybridization requires understanding the ecological, demographic, and phenotypic influences on mate choice in hybridizing taxa. Here, I review how these influences on mate choice can contribute to hybridization by (1) circumventing (female) choice, (2) bringing formerly isolated species into sympatry, (3) masking cues important for mate recognition, (4) altering the traits or preferences involved in mate recognition, or (5) altering the costs and benefits of mate choice. In particular, hybridization in response to either high direct costs of mate choice or high direct benefits of heterospecific mating may be widespread, a possibility that awaits further testing. Adopting a mate choice perspective to the study of hybridization challenges the assumption of hybrids as reproductive “mistakes” and allows for functional explanations regarding the occurrence and maintenance of hybridization. As evidence of the prevalence and evolutionary importance of animal hybridization accumulates, investigations into the role of behavior will be increasingly important for our understanding of diversification and for conservation applications.     

Why do plants silicify?

Despite seminal papers that stress the significance of silicon (Si) in plant biology and ecology, most studies focus on manipulations of Si supply and mitigation of stresses. The ecological significance of Si varies with different levels of biological organization, and remains hard to capture. We show that the costs of Si accumulation are greater than is currently acknowledged, and discuss potential links between Si and fitness components (growth, survival, reproduction), environment, and ecosystem functioning. We suggest that Si is more important in trait-based ecology than is currently recognized. Si potentially plays a significant role in many aspects of plant ecology, but knowledge gaps prevent us from understanding its possible contribution to the success of some clades and the expansion of specific biomes.     

A review and discussion of platelet nitric oxide and nitric oxide synthase: do blood platelets produce nitric oxide from <Emphasis Type="SmallCaps">l</Emphasis>-arginine or nitrite?

The NO/sGC/cGMP/PKG system is one of the most powerful mechanisms responsible for platelet inhibition. In numerous publications, expression of functional NO synthase (NOS) in human and mouse platelets has been reported. Constitutive and inducible NOS isoforms convert l-arginine to NO and l-citrulline. The importance of this pathway in platelets and in endothelial cells for the regulation of platelet function is discussed since decades. However, there are serious doubts in the literature concerning both expression and functionality of NOS in platelets. In this review, we aim to present and critically evaluate recent data concerning NOS expression and function in platelets, and to especially emphasise potential pitfalls of detection of NOS proteins and measurement of NOS activity. Prevailing analytical problems are probably the main sources of contradictory data on occurrence, activity and function of NOS in platelets. In this review we also address issues of how these problems can be resolved. NO donors including organic nitrites (RONO) and organic nitrate (RONO₂) are inhibitors of platelet activation. Endogenous inorganic nitrite (NO₂ ^?), the product of NO autoxidation, and exogenous inorganic nitrite are increasingly investigated as NO donors in the circulation. The role of platelets in the generation of NO from nitrite is also discussed.     

Why do RNA viruses recombine?

Recombination occurs in many RNA viruses and can be of major evolutionary significance. However, rates of recombination vary dramatically among RNA viruses, which can range from clonal to highly recombinogenic. Here, we review the factors that might explain this variation in recombination frequency and show that there is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction. Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology.