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E Nevo

Publications and source records attributed to E Nevo.

At least 19 recordsLinked to original sources
PubMed2007

Looking for organization patterns of highly expressed genes: purine-pyrimidine composition of precursor mRNAs.

We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNAs of the three targeted gene groups proved to differ significantly from the control. The exons of the three groups tested have higher purine contents and R-tract abundance and lower abundance of Y-tracts compared to the control (R-tract-tract of sequential purines with Rn>or=5; Y-tract-tract of sequential pyrimidines with Yn>or=5). In species widely employing "intron definition" in the splicing process, the Y content of introns of the three targeted groups appeared to be higher compared to the control group. Furthermore, in all examined species, the introns of the targeted genes have a lower abundance of R-tracts compared to the control. We hypothesized that the R-Y composition of the targeted gene groups contributes to high rate and efficiency of both splicing and translation, in addition to the mRNA coding role. This is presumably achieved by (1) reducing the possibility of the formation of secondary structures in the mRNA, (2) using the R-tracts and R-biased sequences as exonic splicing enhancers, (3) lowering the amount of targets for pyrimidine tract binding protein in the exons, and (4) reducing the amount of target sequences for binding of serine/arginine-rich (SR) proteins in the introns, thereby allowing SR proteins to bind to proper (exonic) targets.

Animals↗
PubMed2006

P53 in blind subterranean mole rats--loss-of-function versus gain-of-function activities on newly cloned Spalax target genes.

A tumor suppressor gene, p53, controls cellular responses to a variety of stress conditions, including DNA damage and hypoxia, leading to growth arrest and/or apoptosis. Recently, we demonstrated that in blind subterranean mole rats, Spalax, a model organism for hypoxia tolerance, the p53 DNA-binding domain contains a specific Arg174Lys amino acid substitution. This substitution reduces the p53 effect on the transcription of apoptosis genes (apaf1, puma, pten and noxa) and enhances it on human cell cycle arrest and p53 stabilization/homeostasis genes (mdm2, pten, p21 and cycG). In the current study, we cloned Spalax apaf1 promoter and mdm2 intronic regions containing consensus p53-responsive elements. We compared the Spalax-responsive elements to those of human, mouse and rat and investigated the transcriptional activity of Spalax and human Arg174Lys-mutated p53 on target genes of both species. Spalax and human-mutated p53 lost induction of apaf1 transcription, and increased induction of mdm2 transcription. We conclude that Spalax evolved hypoxia-adaptive mechanisms, analogous to the alterations acquired by cancer cells during tumor development, with a bias against apoptosis while favoring cell arrest and DNA repair.

Animals↗
PubMed2006

Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from "Evolution Canyon": microsatellite polymorphism, ploidy and controversial sexual status.

The yeast S. cerevisiae is a central model organism in eukaryotic cell studies and a major component in many food and biotechnological industrial processes. However, the wide knowledge regarding genetics and molecular biology of S. cerevisiae is based on an extremely narrow range of strains. Studies of natural populations of S. cerevisiae, not associated with human activities or industrial fermentation environments, are very few. We isolated a panel of S. cerevisiae strains from a natural microsite, "Evolution Canyon" at Mount Carmel, Israel, and studied their genomic biodiversity. Analysis of 19 microsatellite loci revealed high allelic diversity and variation in ploidy level across the panel, from diploids to tetraploids, confirmed by flow cytometry. No significant differences were found in the level of microsatellite variation between strains derived from the major localities or microniches, whereas strains of different ploidy showed low similarity in allele content. Maximum genetic diversity was observed among diploids and minimum among triploids. Phylogenetic analysis revealed clonal, rather than sexual, structure of the triploid and tetraploid subpopulations. Viability tests in tetrad analysis also suggest that clonal reproduction may predominate in the polyploid subpopulations.

Alleles↗
PubMed2006

Laccase and manganese peroxidase activities of Phellinus robustus and Ganoderma adspersum grown on food industry wastes in submerged fermentation.

Phellinus robustus produced both laccase (700-4,000 U l(-1)) and manganese peroxidase (MnP) (1,000-11,300 U l(-1)) in fermentation of nine food wastes, whereas Ganoderma adspersum produced only laccase (600-34,000 U l(-1)). Glucose provided high laccase and MnP activity of P. robustus but repressed enzyme production by G. adspersum. Ammonium sulphate and ammonium tartrate increased the P. robustus laccase yield (3-fold), whereas the accumulation of MnP was not enhanced by additional nitrogen.

Animals↗
PubMed2006

Adaptive differentiation of thermotolerance in Drosophila along a microclimatic gradient.

We examined whether a remarkable occurrence - the physiological evolution of two Drosophila melanogaster populations, despite a spatial separation of only 100-400 m, was idiosyncratic and temporary, or persisted over multiple years. We ascertained the high-temperature tolerance of Drosophila descended from populations on the north-facing slope (NFS) and south-facing slope (SFS) of 'Evolution Canyon' (Lower Nahal Oren, Mt Carmel, Israel), which were collected in 1997, 1999, and 2000. Results for these Drosophila uniformly resembled other studies in many respects: an inverse relationship between survival and heat-shock temperature, male-female differences in thermotolerance, and inducible thermotolerance. Importantly, for all years of collection, SFS flies consistently exceeded NFS flies in basal and inducible thermotolerance after diverse heat shocks, with and without thermal pretreatment, and whether isofemale lines, synthetic populations, or inbred lines were compared. Inbred lines, however, had lower thermotolerance than outbred lines. Several nonexclusive processes may explain the evolution of such physiological differentiation.

Acclimatization↗
PubMed2006

Heparanase neutralizes the anticoagulation properties of heparin and low-molecular-weight heparin.

BACKGROUND: Heparanase is a mammalian endo-D-glucuronidase that cleaves heparan sulfate (HS) in the extracellular matrix and cell surface. It is preferentially expressed by cells of the immune system and tumor cells. Heparanase overexpression in experimental tumor models results in increased angiogenesis and metastasis. Heparin and low-molecular weight heparin (LMWH) inhibit HS degradation by heparanase. OBJECTIVE: To investigate whether heparanase cleaves heparin and LMWH, and elucidate its effect on blood coagulation. METHODS: Heparin and LMWH were incubated with recombinant heparanase and subjected to measurements of molecular size (size exclusion chromatography) and anticoagulant activity (plasma APTT-activated thromboplastin time, and anti-Xa activity). APTT was also measured in plasma samples of transgenic mice overexpressing heparanase, in comparison with control mice. RESULTS: Incubation of heparin and LMWH with heparanase resulted in degradation of these substrates, as revealed by a significant decrease in their molecular weight. This was correlated with a marked suppression of the anticoagulant activity of heparin and LMWH, as indicated by a decreased effect on APTT and anti-Xa activity, respectively, when human plasma was added. Transgenic mice overexpressing heparanase exhibited a significantly shorter APTT than control mice. CONCLUSION: Heparanase is capable of degrading heparin and LMWH, so that its overexpression by tumor cells may contribute to heparin resistance, commonly occurring in cancer patients. In view of the complexity of the currently available heparanase activity assays, we propose an indirect approach to quantify heparanase activity by measuring the decrease in plasma APTT or anti-Xa activity exerted by the enzyme under the defined conditions.

Animals↗
PubMed2005

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression.

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

Adaptation, Physiological↗
PubMed2005

Coevolution of DNA-interacting proteins and genome "dialect".

Several species-specific characteristics of genome organization that are superimposed on its coding aspects were proposed earlier, including genome signature (GS), genome accent, and compositional spectrum (CS). These notions could be considered as representatives of genome dialect (GD). We measured within the Proteobacteria some GD representatives, the relative abundance of dinucleotides or GS, the profiles of occurrence of 10 nucleotide words (CS), and the profiles of occurrence of 20 nucleotide words, using a degenerate two-letter alphabet (purine-pyrimidine compositional spectra [PPCS]). Here, we show that the evolutionary distances between DNA repair and recombination orthologous enzymes (especially those of the nucleotide excision repair system) are highly correlated with PPCS and GS distances. Orthologous proteins involved in structural or metabolic processes (control group) have significantly lower correlations of their evolutionary distances with the PPCS and GS distances. We hypothesize that the high correlation of the evolutionary distances of the DNA repair orthologous enzymes with their GD is a result of the coevolution of the DNA repair enzymes' structures and GDs. Species GDs could be substantially influenced by the function of DNA polymerase I (the bacterial major DNA repair polymerase). This might cause the correlation of species GDs differentiation with evolutionary changes of species DNA polymerase I. Simultaneously, the structures of DNA repair-recombination enzymes might be evolutionarily sensitive and responsive to changes in the structure of their substrate-the DNA (including those that are represented by GD differentiation). We further discuss the rationale and mechanisms of the hypothesized coevolution. We suggest that stress might be an important cause of changes in the repair-recombination genes and the GD and the trigger of the aforementioned coevolution process. Other triggers might be massive horizontal gene transfer and ecological selection.

DNA Repair↗
PubMed2005

Carbon and nitrogen sources influence the ligninolytic enzyme activity of Trametes versicolor.

Among carbon sources studied, cellobiose and mannitol provided the highest laccase (Lac) activity (648 and 742 U1(-1), respectively) of Trametes versicolor 775 while glucose gave maximum manganese peroxidase (MnP) and peroxidase activities (44 and 114 U1(-1), respectively). Citrus fruit peel as growth substrate enhanced Lac activity 7-fold when compared to the medium with cellobiose, whereas grape vine sawdust increased MnP and peroxidase activity up to 148 and 677 U1(-1), respectively.

Carbohydrates↗
PubMed2005

Emmonsiosis of subterranean rodents (Bathyergidae, Spalacidae) in Africa and Israel.

The presence of adiaspores of the fungal genus Emmonsia was examined in the lungs of 85 mole rats representing 3 subterranean genera: blind mole rats (Spalax galili and S. golani) from Israel, Ansell's mole-rats (Cryptomys anselli) from Zambia, and silvery mole-rats (Heliophobius argenteocinereus) from Malawi and Zambia. Emmonsiosis was found in 28% of the blind mole rats, 100% of the Ansell's mole-rats, but in none of the silvery mole-rats. Infection in African mole-rats was caused by Emmonsia parva, and infection in Israeli blind mole rats was caused by E. parva and E. crescens. The study indicates that the perennial burrow system of the Ansell's mole-rat forms an appropriate microhabitat for the saprophytic growth of E. parva in Lusaka region, Zambia. We suggest that factors contributing to the striking difference in prevalence of emmonsiosis between the two African mole-rat genera (Cryptomys, Heliophobius) may be their differing burrow types, burrow longevity, and social lives.

Africa↗
PubMed2005

Sequence polymorphism of candidate behavioural genes in Drosophila melanogaster flies from 'Evolution canyon'.

This study focuses on the molecular features of three candidate behavioural genes in Drosophila melanogaster from the opposite slopes of Nahal Oren Canyon, Mount Carmel, Israel. These slopes display dramatic physical and biotic contrasts. Spatial variation of microclimatic conditions leads to adaptive differentiation and partial sexual isolation of populations, as suggested by our previous studies. The chosen candidate genes presumably contributing to genetic variation in sexual behaviour of Drosophila in the Canyon were desaturase, period, and no-on-transient A. These genes are known to include polymorphic repeated sequences, insertions/deletions, or nucleotide substitutions. The idea was that their polymorphism might be one of the determinants of behavioural peculiarities of flies derived from the opposite slopes. Indeed, interslope differences in the sequence encoding the (Thr-Gly)n repeat (exon 5) of the period gene were established, suggesting evolutionary functional importance. In particular, we unraveled variation in the length and composition of this region in different NFS (north-facing slope) and SFS (south-facing slope) lines. The 'European' allele (n = 20) was a 2.6-fold more abundant on the NFS compared to the SFS. This predominance probably gives some advantages for flies inhabiting wet and less warm conditions of the NFS. We suggest that repeat length/composition may influence the functional features of flies, i.e. habitat choice, nonrandom mating, and temperature adaptation. A series of female single-mate-choice tests show that females derived from NFS distinguish between males with specific per alleles (n = 17 vs. n = 20), as well as between males originated from the opposing slopes. Females from SFS were less discriminating and did not manifest significant deviation from random mating.

Animals↗
PubMed2005

Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species.

Here, we report data on the population variability of Ty3-gypsy retrotransposons in genomes of Aegilops speltoides (2n = 2x = 14) and Hordeum spontaneum (2n = 2x = 14). Based on the sequence analysis or reverse transcriptase (RT) gene conserved domains, two groups of elements were recognized. Elements of Group I show relatedness to such a known element as RIRE2, and elements of Group II show relatedness to Fatima and Cereba. Cloned and sequenced fragments of Ty3-gypsy RT that show the closest relatedness to known elements (Fatima and RIRE2) were used as probes for fluorescent in situ hybridization (FISH). FISH experiments revealed mini-cluster organization of the Ty3-gypsy element chromosomal distribution in wild Triticeae species. Mini-clusters can be divided into three categories according to their intraspecific stability: (i) stable species-specific clusters that are mainly adjusted to the regions of rRNA genes; (ii) variable clusters that represent 68% of clusters in the genome of Ae. speltoides and 20% in the genome of H. spontaneum; and (iii) population-specific clusters that are mainly insertions into centromeric central domains of different chromosomes and the majority of these insertions were detected in populations with hot, dry environments. Significant interpopulation variability of Ty3-gypsy element chromosomal distribution in the Ae. speltoides genome contrasts with the uniform genome of H. spontaneum and may reflect differences in adaptive strategies between investigated species.

Base Sequence↗
PubMed2005

Heterochromatin differentiation shows the pathways of karyotypic evolution in Israeli mole rats (Spalax, Spalacidae, Rodentia).

C-banding, base-specific fluorochrome staining (CMA3/DA/DAPI), and comparative genomic hybridization (CGH) were used to analyze the constitutive heterochromatin in two Israeli Spalax species, S. galili (2n = 52) and S. judai (2n = 60). It was shown that C-positive centromeric heterochromatin and some telomeric sites comprise GC-rich DNA sequences in both species. Comparative genomic in situ hybridization revealed slight qualitative differences in highly repetitive sequences in the two Spalax species. Eight acrocentric pairs in S. judai that are involved in Robertsonian rearrangements, possessed composite heterochromatin with a preference of S. judai highly repetitive sequences in the proximal region. Heterochromatin of the sex chromosomes, two biarmed homologous pairs (4 and 5) in both species, and acrocentric chromosomes from the group with a variable centromere position in S. judai was entirely species-specific. The high level of homology in the composition of heterochromatin may relate to the recent divergence of Israeli Spalax. Interspecies heterochromatin differences are discussed in the context of possible mechanisms in the Spalax chromosome evolution.

Animals↗
PubMed2004

Genetic basis of barley caryopsis dormancy and seedling desiccation tolerance at the germination stage.

The genomic regions controlling caryopsis dormancy and seedling desiccation tolerance were identified using 152 F4 lines derived from a cross between Mona, a Swedish cultivar, and an Israeli xeric wild barley Hordeum spontaneum genotype collected at Wadi Qilt, Israel. Dormancy, the inability of a viable seed to germinate, and desiccation tolerance, the ability of the desiccated seedlings to revive after rehydration, were characterized by fitting the germination and revival data with growth curves, using three parameters: minimum, maximum, and slope of germination or revival rate derived by the least square method. The genetic map was constructed with 85 genetic markers (SSRs, AFLPs, STSs, and Dhn genes) using the MULTIPOINT: -mapping algorithm. Quantitative trait loci (QTLs) mapping was conducted with the MULTIQTL: package. Ten genomic regions were detected that affected the target traits, seven of which affected both dormancy and desiccation tolerance traits. Both the wild barley genotype and the Swedish cultivar contributed the favorite alleles for caryopsis dormancy, whereas seedling desiccation tolerance was attributed to alleles descending from the cultivar. The results indicate that some barley dormancy genes are lost during domestication and that dormancy QTLs are associated with abiotic stress tolerance.

Chromosome Mapping↗
PubMed2004

Fast and high precision algorithms for optimization in large-scale genomic problems.

There are several very difficult problems related to genetic or genomic analysis that belong to the field of discrete optimization in a set of all possible orders. With n elements (points, markers, clones, sequences, etc.), the number of all possible orders is n!/2 and only one of these is considered to be the true order. A classical formulation of a similar mathematical problem is the well-known traveling salesperson problem model (TSP). Genetic analogues of this problem include: ordering in multilocus genetic mapping, evolutionary tree reconstruction, building physical maps (contig assembling for overlapping clones and radiation hybrid mapping), and others. A novel, fast and reliable hybrid algorithm based on evolution strategy and guided local search discrete optimization was developed for TSP formulation of the multilocus mapping problems. High performance and high precision of the employed algorithm named guided evolution strategy (GES) allows verification of the obtained multilocus orders based on different computing-intensive approaches (e.g., bootstrap or jackknife) for detection and removing unreliable marker loci, hence, stabilizing the resulting paths. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on simulated data of multilocus genetic maps up to 1000 points per linkage group.

Algorithms↗
PubMed2004

Differential selection of growth rate-related traits in wild barley, Hordeum spontaneum, in contrasting greenhouse nutrient environments.

Across-species comparisons show that inherent variation in relative growth rate (RGR) and its underlying traits are correlated with habitat productivity. In this study, we test the hypothesis that growth rate-related traits confer differential selective effects in contrasting nutrient environments. We specifically test whether high RGR is targeted by selection in nutrient-rich environments whereas low values of traits that underlie RGR [specific leaf area (SLA), leaf mass fraction and leaf area ratio (LAR)] confer a direct fitness advantage in nutrient-poor environments, resulting in selection of low RGR as a correlated response. We measured RGR, its underlying component traits, and estimated fitness in a range of wild barley (Hordeum spontaneum) accessions grown under high and low nutrient conditions. Selection on component traits differed between the two environments, while total selection of RGR was not significant. Using multiple regression and path analysis to estimate direct fitness effects, a selective advantage of high LAR and SLA was demonstrated only under nutrient-rich conditions. While supporting the view that observed associations between habitat richness and some RGR-component traits reflect adaptation to differing nutrient regimes, our data suggest that direct selection targets component traits rather than RGR itself.

Analysis of Variance↗
PubMed2003

Efficient multipoint mapping: making use of dominant repulsion-phase markers.

The paper is devoted to the problem of multipoint gene ordering with a particular focus on "dominance" complication that acts differently in conditions of coupling-phase and repulsion-phase markers. To solve the problem we split the dataset into two complementary subsets each containing shared codominant markers and dominant markers in the coupling-phase only. Multilocus ordering in the proposed algorithm is based on pairwise recombination frequencies and using the well-known travelling salesman problem (TSP) formalization. To obtain accurate results, we developed a multiphase algorithm that includes synchronized-marker ordering of two subsets assisted by re-sampling-based map verification, combining the resulting maps into an integrated map followed by verification of the integrated map. A new synchronized Evolution-Strategy discrete optimization algorithm was developed here for the proposed multilocus ordering approach in which common codominant markers facilitate stabilization of the marker order of the two complementary maps. High performance of the employed algorithm allows systematic treatment for the problem of verification of the obtained multilocus orders, based on computing-intensive bootstrap and jackknife technologies for detection and removing unreliable marker scores. The efficiency of the proposed algorithm was demonstrated on simulated and real data.

Algorithms↗