Using bleach-chase to measure protein half-lives in living cells

Protein removal has a central role in numerous cellular processes. Obtaining systematic measurements of multiple protein removal rates is necessary to understand the principles that govern these processes, but it is currently a major technical challenge. To address this, we developed 'bleach-chase', a noninvasive method for measuring the half-lives of multiple proteins at high temporal resolution in living cells. The method uses a library of annotated human reporter cell clones, each with a unique fluorescently tagged protein expressed from its native chromosomal location. In this protocol, we detail a simple procedure that bleaches the cells and uses time-lapse fluorescence microscopy and automated image analysis to systematically measure the half-life dynamics of multiple proteins. The duration of the protocol is 4-5 d. The method may be applicable to a wide range of fluorescently tagged proteins and cell lines.     

Jack of all trades, master of all: a positive association between habitat niche breadth and foraging performance in pit-building antlion larvae

Species utilizing a wide range of resources are intuitively expected to be less efficient in exploiting each resource type compared to species which have developed an optimal phenotype for utilizing only one or a few resources. We report here the results of an empirical study whose aim was to test for a negative association between habitat niche breadth and foraging performance. As a model system to address this question, we used two highly abundant species of pit-building antlions varying in their habitat niche breadth: the habitat generalist Myrmeleon hyalinus, which inhabits a variety of soil types but occurs mainly in sandy soils, and the habitat specialist Cueta lineosa, which is restricted to light soils such as loess. Both species were able to discriminate between the two soils, with each showing a distinct and higher preference to the soil type providing higher prey capture success and characterizing its primary habitat-of-origin. As expected, only small differences in the foraging performances of the habitat generalist were evident between the two soils, while the performance of the habitat specialist was markedly reduced in the alternative sandy soil. Remarkably, in both soil types, the habitat generalist constructed pits and responded to prey faster than the habitat specialist, at least under the temperature range of this study. Furthermore, prey capture success of the habitat generalist was higher than that of the habitat specialist irrespective of the soil type or prey ant species encountered, implying a positive association between habitat niche-breadth and foraging performance. Alternatively, C. lineosa specialization to light soils does not necessarily confer upon its superiority in utilizing such habitats. We thus suggest that habitat specialization in C. lineosa is either an evolutionary dead-end, or, more likely, that this species' superiority in light soils can only be evident when considering additional niche axes.     

Nitric-oxide supplementation for treatment of long-term complications in argininosuccinic aciduria

Argininosuccinate lyase (ASL) is required for the synthesis and channeling of L-arginine to nitric oxide synthase (NOS) for nitric oxide (NO) production. Congenital ASL deficiency causes argininosuccinic aciduria (ASA), the second most common urea-cycle disorder, and leads to deficiency of both ureagenesis and NO production. Subjects with ASA have been reported to develop long-term complications such as hypertension and neurocognitive deficits despite early initiation of therapy and the absence of documented hyperammonemia. In order to distinguish the relative contributions of the hepatic urea-cycle defect from those of the NO deficiency to the phenotype, we performed liver-directed gene therapy in a mouse model of ASA. Whereas the gene therapy corrected the ureagenesis defect, the systemic hypertension in mice could be corrected by treatment with an exogenous NO source. In an ASA subject with severe hypertension refractory to antihypertensive medications, monotherapy with NO supplements resulted in the long-term control of hypertension and a decrease in cardiac hypertrophy. In addition, the NO therapy was associated with an improvement in some neuropsychological parameters pertaining to verbal memory and nonverbal problem solving. Our data show that ASA, in addition to being a classical urea-cycle disorder, is also a model of congenital human NO deficiency and that ASA subjects could potentially benefit from NO supplementation. Hence, NO supplementation should be investigated for the long-term treatment of this condition.     

Rapid divergence of microsatellite abundance among species of Drosophila

Among major taxonomic groups, microsatellites exhibit considerable variation in composition and allele length, but they also show considerable conservation within many major groups. This variation may be explained by slow microsatellite evolution so that all species within a group have similar patterns of variation, or by taxon-specific mutational or selective constraints. Unfortunately, comparing microsatellites across species and studies can be problematic because of biases that may exist among different isolation and analysis protocols. We present microsatellite data from five Drosophila species in the Drosophila subgenus: D. arizonae, D. mojavensis, and D. pachea (three cactophilic species), and D. neotestacea and D. recens (two mycophagous species), all isolated at the same time using identical protocols. For each species, we compared the relative abundance of motifs, the distribution of repeat size, and the average number of repeats. Dimers were the most abundant microsatellites for each species. However, we found considerable variation in the relative abundance of motif size classes among species, even between sister taxa. Frequency differences among motifs within size classes for the three cactophilic species, but not the two mycophagous species, are consistent with other studied Drosophila. Frequency distributions of repeat number, as well as mean size, show significant differences among motif size classes but not across species. Sizes of microsatellites in these five species are consistent with D. virilis, another species in the subgenus Drosophila, but they have consistently higher means than in D. melanogaster, in the subgenus Sophophora. These results confirm that many aspects of microsatellite variation evolve quickly but also are subject to taxon-specific constraints. In addition, the nature of microsatellite evolution is dependent on temporal and taxonomic scales, and some variation is conserved across broad taxonomic levels despite relatively high rates of mutation for these loci.     

CD66a interactions between human melanoma and NK cells: a novel class I MHC-independent inhibitory mechanism of cytotoxicity

NK cells are able to kill virus-infected and tumor cells via a panel of lysis receptors. Cells expressing class I MHC proteins are protected from lysis primarily due to the interactions of several families of NK receptors with both classical and nonclassical class I MHC proteins. In this study we show that a class I MHC-deficient melanoma cell line (1106mel) is stained with several Ig-fused lysis receptors, suggesting the expression of the appropriate lysis ligands. Surprisingly, however, this melanoma line was not killed by CD16-negative NK clones. The lack of killing is shown to be the result of homotypic CD66a interactions between the melanoma line and the NK cells. Furthermore, 721.221 cells expressing the CD66a protein were protected from lysis by YTS cells and by NK cells expressing the CD66a protein. Redirected lysis experiments demonstrated that the strength of the inhibitory effect is correlated with the levels of CD66a expression. Finally, the expression of CD66a protein was observed on NK cells derived from patients with malignant melanoma. These findings suggest the existence of a novel class I MHC-independent inhibitory mechanism of human NK cell cytotoxicity. This may be a mechanism that is used by some of the class I MHC-negative melanoma cells to evade attack by CD66a-positive NK cells.     

Evaluation of the predictive power of calculation procedure for molecular hydrophobicity of some estradiol derivates

Several calculation procedures for log P values based on the fragmental and atomic contributions are compared with experimental reversed-phase liquid chromatography (RPLC) retention of estradiol derivates. The RPLC experiments were performed on HPTLC and HPLC commercially available stationary phases. Binary solvent mixtures of methanol-water and acetonitrile-water were used as mobile phases. The correlation between log P and various chromatographically obtained hydrophobicity parameters (R(M)0, log k(w) and phi0) are quantified. The R(M)0, i.e., log k(w) were obtained by linear extrapolation of retention to 0% organic modifier. Phi0 values were obtained from the slopes and intercepts of such linear relationship. The mutual relationship between phi(0,MeOH) and phi(0,ACN) values of the compounds were discussed. The obtained statistical results can be summarized in the following order of reliabilities for different log P calculation methods: Broto>ACD/logP>Crippen>Rekker>Viswanadhan.     

Computational model of the cockroach escape behavior: winner and losers in a population code

 I present a comprehensive biologically oriented computational model to account for the escape response of the cockroach on the ground. This model is an expansion of previous work that accounted only for discriminating left from right wind directions [Ezrachi et al. (1999) Biol Cybern 81: 89–99]. The model is composed of computational elements describing the biological processes taking place in the various neurons and includes input which emulates empirical data. With this model it is possible to obtain escape behavior that resembles natural behavior. The model is used to address an ongoing debate as to whether the cockroach's turn direction is determined by computations carried out by the entire neuronal population (PC) or rather by a “winner-take-all” (WTA) mechanism. I suggest that the computation mechanism that underlies the cockroach escape response is composed of both PC and WTA principles. Based on the properties of the suggested new mechanism I denote it a “Darwinian population code.” Received: 26 March 2002 / Accepted in revised form: 24 June 2002 Acknowledgements. I thank H. Parnas for her advice and assistance, J. M. Camhi for helpful comments, and D. Lipson for developing the simulation tools. Correspondence to: E. A. Ezrachi (e-mail: erez@piano.ls.huji.ac.il, Tel.: +972-2-6585818, Fax: +972-2-6585569)     

Experience of time with mental disorder

The aim of research was to examine subjective experience of time with examinees with diagnosed schizophrenia and examinees with diagnosed neurotic disorder. Differences inside those two diagnostic categories of mental disorders, and differences u compare to examinees without diagnosed mental disorder were explored. For needs of research questionnaire was constructed accordingly to available data from literature. In research participated examinees from 30-50 of age, which were equaled by age and gender. Research was performed on three groups, first group was made of examinees with diagnosed schizophrenic disorder (n=43), second group was made of examinees with diagnosed neurotic disorder (n=40), and third group consisted of examines without mental disorder (n=39). Results of examination have showed significant statistical differences between certain groups considering particles of poll requester. Differences in subjective experience of time were presented according to items from questionnaire. Mutual for both groups of examinees with mental disorder is existence of pathological deviation in anticipating future. This was manifested in different ways and levels, depending of mental disorder. Given results confirm assumption that capability of anticipating future is important fact of mature and healthy individual.     

Contrasting population genetic patterns and evolutionary histories among sympatric Sonoran Desert cactophilic Drosophila

We studied population genetic differentiation in the sympatric Sonoran Desert cactophilic flies Drosophila pachea, D. mettleri and D. nigrospiracula across their continental and peninsular ranges. These flies show marked differences in ecology and behaviour including dispersal distances and host cactus specialization. Examination of a fragment of the mitochondrial cytochrome oxidase subunit I gene (mtCOI) reveals that the Sea of Cortez has constituted an effective dispersal barrier for D. pachea, leading to significant genetic differentiation between the continental and peninsular ranges of this species. No genetic differentiation was detected, however, within its continental and peninsular ranges. In contrast, our mtCOI-based results for D. mettleri and D. nigrospiracula are consistent with a previous allozyme-based study that showed no significant genetic differentiation between continental and peninsular ranges of these two species. For D. mettleri, we also found that the insular population from Santa Catalina Island, California, is genetically differentiated with respect to continental and peninsular localities. We discuss how differences in the genetic structure patterns of D. pachea, D. mettleri and D. nigrospiracula may correspond to differences in their dispersal abilities, host preferences and behaviour.