Interaction of MAR-sequences with nuclear matrix proteins.

The recent discovery of DNA sequences responsible for the specific attachment of chromosomal DNA to the nuclear skeleton (MARs/SARs) was an important step towards our understanding of the functional and structural organization of eukaryotic chromatin [Mirkovitch et al.: Cell 44:273-282, 1984; Cockerill and Garrard: Cell 44:273-282, 1986]. A most important question, however, remains the nature of the matrix proteins involved in the specific binding of the MARs. It has been shown that topoisomerase II and histone H1 were capable of a specific interaction with SARs by the formation of precipitable complexes [Adachi et al.: EMBO J8:3997-4006, 1989; Izaurralde et al.: J Mol Biol 210:573-585, 1989]. Here, applying a different approach, we were able to "visualize" some of the skeletal proteins recognizing and specifically binding MAR-sequences. It is shown that the major matrix proteins are practically the same in both salt- and LIS-extracted matrices. However, the relative MAR-binding activity of the individual protein components may be different, depending on the method of matrix preparation. The immunological approach applied here allowed us to identify some of the individual MAR-binding matrix proteins. Histone H1 and nuclear actin are shown to be not only important components of the matrix, but to be involved in a highly efficient interaction with MAR-sequences as well. Evidence is presented that proteins recognized by the anti-HMG antibodies also participate in MAR-interactions.     

Phylogeography of the temperate grassland plant Tephroseris kirilowii (Asteraceae) inferred from multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) data

Journal of Plant Research - A group of temperate grassland plant species termed the “Mansen elements” occurs in Japan and is widely distributed in the grasslands of continental East...     

Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.

Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.     

Gene identification in a complex chromosomal continuum by local genomic cross-referencing

Most higher plants have complex genomes containing large quantities of repetitive DNA interspersed with low-copy-number sequences. Many of these repetitive DNAs are mobile and have homology to RNAs in various cell types. This can make it difficult to identify the genes in a long chromosomal continuum. It was decided to use genic sequence conservation and grass genome co-linearity as tools for gene identification. A bacterial artificial chromosome (BAC) clone containing sorghum genomic DNA was selected using a maize Adh1 probe. The 165 kb sorghum BAC was tested for hybridization to a set of clones representing the contiguous 280 kb of DNA flanking maize Adh1. None of the repetitive maize DNAs hybridized, but most of the low-copy-number sequences did. A low-copy-number sequence that did cross-hybridize was found to be a gene, while one that did not was found to be a low-copy-number retrotransposon that was named Reina. Regions of cross-hybridization were co-linear between the two genomes, but closer together in the smaller sorghum genome. These results indicate that local genomic cross-referencing by hybridization of orthologous clones can be an efficient and rapid technique for gene identification and studies of genome organization.     

A ribonuclease specific for double-stranded RNA and two distinct ribonuclease H activities from the ribosomal salt wash fraction of Ehrlich ascites tumor cells

Three distinct nuclease activities, degrading double-stranded substrates, were isolated from the ribosomal salt wash fraction of Ehrlich ascites tumor cells. One of them is an absolutely Mn²⁺-dependent RNase H, capable of degrading the polyribonucleotide strand of a poly(A) · poly(dT) hybrid only. The other two nuclease activities are: a Mg²⁺-dependent RNase H and a Mn²⁺-dependent ribonuclease, specific for double-stranded RNA. These two activities were inseparable by DEAE-cellulose and phosphocellulose chromatography and both were completely inhibited by 20 mmN-ethymaleimide. It is possible that one protein molecule is responsible for the two activities, depending on the nature of the metal ion, though the existence of two different enzyme molecules is not excluded. The three activities are most probably of extranucleolar origin. A function for the double-stranded RNA-specific enzyme is suggested in the processes regulating protein synthesis. The role of the RNase H activities isolated from the ribosomal salt wash fraction is unclear.     

From obesity to cancer: a review on proposed mechanisms

Nowadays, obesity is considered as a serious and growing global health problem. It is documented that the overweight and obesity are major risk factors for a series of noncommunicable diseases, and in recent years, the obesity‐cancer link has received much attention. Numerous epidemiological studies have shown that obesity is associated with increased risk of several cancer types, including colon, breast, endometrium, liver, kidney, esophagus, gastric, pancreatic, gallbladder, and leukemia, and can also lead to poorer treatment. We review here the epidemiological and experimental evidences for the association between obesity and cancer. Specifically, we discuss potential mechanisms focusing how dysfunctional angiogenesis, chronic inflammation, interaction of proinflammatory cytokines, endocrine hormones, and adipokines including leptin, adiponectin insulin, growth factors, estrogen, and progesterone and strikingly, cell metabolism alteration in obesity participate in tumor development and progression, resistance to chemotherapy, and targeted therapies such as antiangiogenic and immune therapies.     

New Approaches for Absolute Quantification of Stable‐Isotope‐Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag

Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re‐quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2.     

Long-term changes in population genetic features of a rapidly expanding marine invader: implication for invasion success

Large blooms of Rhopilema nomadica, a highly venomous rhizostamatid scyphozoan species introduced to the Mediterranean through the Suez Canal, have become ubiquitous in the summer and winter months along the Israeli coasts since the mid-1980s. This species has since spread across the eastern Mediterranean and was sighted as far west as Tunisia and Sardinia. For the past 12 years, we have studied changes in the mitochondrial COI haplotypes diversity of R. nomadica to investigate small scale fluctuactions of genetic diversity and to reveal possible genetic structuring of the fast spreading invader in the Eastern Mediterranean. The 1091 COI sequences analysed, revealed a highly diverse population displaying 89 haplotypes, 46 of which appeared as singletons, low frequency haplotypes. All the specimens analysed throughout the period belong to a single unstructured population. Though lacking data from the source population in the Red Sea, the high within-population diversity and the high diversity of COI haplotypes support the hypothesis of multiple introductions events, or an open corridor with a continuous influx of propagules. Tajima’s D and Fu’s Fst negative values and the increased numbers of COI singletons from early to late sampling periods, have verified that the Israeli population is characterized by a rapid expanding population. Further research is needed for the evaluation of COI diversity and patterns in R. nomadica populations across the eastern Mediterranean Sea and Red Sea, as well as any correlation of the high variability between COI locus and phenotypic diversity.