Chromosome-specific alpha satellites: two distinct families on human chromosome 18.

Two types of human chromosome 18-specific alpha satellite fragments have been cloned and sequenced. They represent closely related but distinct alphoid families formed by two different types of the higher-order repeated units (1360-bp EcoRI and 1700-bp HindIII fragments) that do not alternate in the genome. The individual repeats within each family are 99% identical and interfamily homology is about 78%. Sequence analysis shows that both repeats belong to alphoid suprachromosomal family 2, but their homology is not higher than that of family members located on different chromosomes. Therefore, the two repeats shared a common origin in the recent past, although they are not the direct offspring of one ancestral sequence. Our data indicate that these two 18-specific domains have appeared as a result of two separate amplification events. Despite the high degree of homology, they are not undergoing intrachromosomal homogenization, although some variation of this process might take place within each domain.     

Scanning and transmission electron microscopy of the squamose gill-filament epithelium from fresh- and seawater adaptedTilapia

Synopsis The architecture of the gill structure of variousTilapia species was studied in relation to their adaptability to hypersaline media. Using SEM and EM, it was shown that the squamose epithelial cells of the gills have species-typical patterns of ridges on their outer surfaces. These have previously been misinterpreted by other authors as microvilli or stereocillia. The ridges are more dense and better developed in euryhaline species, likeT. zillii, and less so in stenohaline species likeSarotherodon niloticus. Comparing freshwater and seawater-adapted individuals ofT. zillii, S. niloticus, S. galflaeus, andTristramella sacra, it was shown that in fresh water the surface cells are slightly swollen, extending over the openings of the chloride cells. During adaptation to sea water, these ridges become higher and denser and the cell surface shrinks, exposing the underlying orifices of the apical crypts of the chloride cells. The more euryhaline the species, the less change there is in the ridge pattern of the cells during passage from fresh to sea water. This evidence implicates the gill epithelium, together with the chloride cells, in the process of osmoregulation.     

Glutamine-stimulated amino acid and peptide incorporation in Bacteroides melaninogenicus.

The uptake of a number of amino acids and dipeptides by cells and spheroplasts of Bacteroides melaninogenicus was stimulated by the presence of glutamine; 50 mM glutamine induced maximum uptake of glycine or alanine, and glutamine stimulated the uptake of glycine over a wide concentration range (0.17 to 170 mM). Glutamine stimulated the uptake of the dipeptides glycylleucine and glycylproline at significantly faster rates compared with glycine and leucine. The amino acids whose uptake was stimulated by glutamine were incorporated into trichloroacetic acid-precipitable material, and the inclusion of chloramphenicol or puromycin did not affect this incorporation. The uptake of glutamine by cells was concentration dependent. In contrast, in the absence of chloramphenicol 79% of the glutamine taken up by cells supplied with a high external concentration (4.4 mM) was trichloroacetic acid soluble. Glutamate and alpha-ketoglutarate were identified in the intracellular pool of glutamine-incubated spheroplasts. The amino acids and peptides were incorporated into cell envelope material, and a portion (30 to 50%) of the incorporated amino acids could be removed by trypsinization or treatment with papain. The effect of glutamine was depressed by inhibitors of energy metabolism, suggesting that glutamine-stimulated incorporation is an energy-mediated effect.     

Role of nucleosides, 5-phosphoribosyl-1-pyrophosphate, and ribose 1-phosphate in the biosynthesis of phosphosphingolipids in Bacteroides melaninogenicus.

Using a deenergized spheroplast system from Bacterioides melaninogenicus, the sphingolipid precursor 3-ketodihydrosphingosine is not incorporated into the complete sphingolipids, ceramide phosphorylethanolamine, or ceramide phosphorylglycerol unless supplied with glutamine, ATP, ADP, or AMP. Adenosine, inosine, and certain other nucleosides were as effective as ATP. Purine bases and ribose, however, were inactive in this system. 5-Phosphoribosyl-1-pyrophosphate and ribose 1-phosphate also stimulated conversion of 3-ketodihydrosphingosine into ceramide phosphorylethanolamine and ceramide phosphorylglycerol, whereas ribose 5-phosphate showed only slight activity. Hypoxanthine was the main product formed from inosine and adenosine but there was no evidence for nucleotide formation. Adenosine stimulated³²P_i incorporation into cell phospholipids indicating that ribose 1-phosphate, formed via purine nucleoside phosphorylase, could be the compound stimulating sphingolipid synthesis in this system.     

On the synthesis of viral ribonucleic acids and ribonucleoproteins in the submitochondrial system completely free of interfering cytoplasmic contaminations

Summary The synthesis of virus-specific macromolecules was studied in the reconstituted system containing inner membrane-matrix fraction from rat liver mitochondria and infectious RNA of Venezuelian equine encephalomyelitis (VEE) virus. In a series of preliminary experiments it was shown that isolated submitochondrial fraction was completely free of interfering cytoplasmic contaminations and particularly, of cytoplasmic 80S ribosomes. VEE RNA when added to submitochondrial system caused significant stimulation of RNA and protein synthesis. These processes were resistant to actinomycin D which inhibited profoundly the synthesis of proper mitochondrial macromolecules. The stimulating effect of VEE RNA in experiments with submitochondrial system was about three times higher than that with intact mitochondria. The stimulation of¹⁴C-amino acid incorporation increased as a function of incubation time; a certain lag-period being observed. The newly formed virus-specific RNA's and ribonucleoproteins were identified with the aid of sedimentation analysis. In particular, radioactive RNA's with sedimentation coefficients 40S and 26-18S were isolated from the incubated system. These RNA's are similar respectively to VEE genome RNA and doublestranded VEE replicative RNA. In double labelling experiments with³H-uridine and¹⁴Camino acids it was shown that VEE RNA induced synthesis of ribonucleoproteins containing newly formed RNA and protein. These RNP possessed sedimentation coefficients 60-80S, 140S and 300S in sucrose gradient and buoyant densities 1.32 and 1.50 g/cm³ in cesium chloride gradients. These properties of ribonucleoproteins synthesized de novo in submitochondrial system are close to those of RNP intermediates of VEE virus reproduction in the infected cells. We concluded that viral RNA could program virus-specific synthesis in the submitochondrial system under conditions that eliminated the contribution of cytoplasmic ribosomes.     

Sensitivity of a Bacteroides melaninogenicus strain to monosaccharides: effect on enzyme induction.

The inhibition of growth in Bacteroides melaninogenicus by sugars in described. Monosaccharides such as D-glucose, D-galactose, D-mannose, and D-fructose are inhibitory at low concentrations, whereas the disaccharides sucrose and lactose are not inhibitory even at high concentrations. The major inhibitory effect of the sugar is found during the transition of lag to logarithmic growth phases. There was no primary effect of D-glucose on protein, ribonucleic acid, or deoxyribonucleic acid synthesis on cells in transition from lag to logarithmic growth. However, the addition of glucose or galactose completely abolished the induction of 3-ketodihydrosphingosine synthetase by vitamin K in vitamin K-depleted cells. Futhermore, in cells which were not vitamin K depleted, the level of this enzyme was drastically reduced by the addition of the sugar. Cyclic adenosine 5-monophosphate was unable to reverse the growth inhibition produced by glucose. In actively growing cultures, addition of sugar slows the growth rate. In these experiments the level of 3-ketodihydrosphingosine synthetase fell only after the cells had assumed the slower rate of growth. There were two indications that D-galactose was more inhibitory than D-glucose; in the presence of 0.1% D-galactose cells in lag phase did not show the increase in turbidity found in similar cells placed in medium with 0.1% D-glucose, and also D-galactose caused a greater decrease in the growth rate of actively growing cultures than was found with D-glucose. These studies suggest that the inhibitory effect of monosaccharides in lag leads to logarithmic growth transition can be ascribed to an effect on enzyme induction. On the other hand, the ability of many monosaccharides to inhibit growth, and the greater inhibitory property of D-galactose compared with D-glucose, suggests that other mechanisms may be operative as well.     

Phenology and polyploidy in annual Brachypodium species (Poaceae) along the aridity gradient in Israel

Local adaptation of plants along environmental gradients provides strong evidence for clinal evolution mediated by natural selection. Plants have developed diverse strategies to mitigate stress, for example, drought escape is a phenological strategy to avoid drought stress, while polyploidy was proposed as a genomic adaptation to stress. Polyploidy as an adaptation to aridity (an environmental parameter integrating temperature and precipitation) was previously documented in annual Brachypodium spp. (Poaceae) in the Western Mediterranean. Here, we examined whether polyploidy or phenology are associated with aridity in annual Brachypodium spp. along the aridity gradient in the Eastern Mediterranean. Using flow cytometry, we determined ploidy levels of plants from natural populations along the Israeli gradient, spanning ∼424 km from mesic Mediterranean to extreme desert climates. In a common garden we recorded time of seedling emergence, flowering and senescence. We tested whether the proportion of allotetraploids in the populations and phenological traits were associated with aridity. Contrary to a previous study in the Western Mediterranean, we found no effect of aridity on the proportion of allotetraploids and diploids within populations. Interestingly, phenology was associated with aridity: time of emergence was later, while flowering and senescence were earlier in desert plants. Our results indicate that in the Eastern Mediterranean, adaptation of Brachypodium to aridity is mediated mainly by phenology, rather than ploidy level. Therefore, we suggest that genome duplication is not the main driver of adaptation to environmental stress; rather, phenological change as a drought escape mechanism may be the major adaptation.     

The phosphatidylinositol‐transfer protein Nir2 binds phosphatidic acid and positively regulates phosphoinositide signalling

Phosphatidic acid (PA) and phosphoinositides are metabolically interconverted lipid second messengers that have central roles in many growth factor (GF)‐stimulated signalling pathways. Yet, little is known about the mechanisms that coordinate their production and downstream signalling. Here we show that the phosphatidylinositol (PI)‐transfer protein Nir2 translocates from the Golgi complex to the plasma membrane in response to GF stimulation. This translocation is triggered by PA formation and is mediated by its C‐terminal region that binds PA in vitro. We further show that depletion of Nir2 substantially reduces the PI(4,5)P2 levels at the plasma membrane and concomitantly GF‐stimulated PI(3,4,5)P3 production. Finally, we show that Nir2 positively regulates the MAPK and PI3K/AKT pathways. We propose that Nir2 through its PA‐binding capability and PI‐transfer activity can couple PA to phosphoinositide signalling, and possibly coordinates their local lipid metabolism and downstream signalling.     

Deficiency of the Cog8 Subunit in Normal and CDG‐Derived Cells Impairs the Assembly of the COG and Golgi SNARE Complexes

Multiple mutations in different subunits of the tethering complex Conserved Oligomeric Golgi (COG) have been identified as a cause for Congenital Disorders of Glycosylation (CDG) in humans. Yet, the mechanisms by which COG mutations induce the pleiotropic CDG defects have not been fully defined. By detailed analysis of Cog8 deficiency in either HeLa cells or CDG‐derived fibroblasts, we show that Cog8 is required for the assembly of both the COG complex and the Golgi Stx5‐GS28‐Ykt6‐GS15 and Stx6‐Stx16‐Vti1a‐VAMP4 SNARE complexes. The assembly of these SNARE complexes is also impaired in cells derived from a Cog7‐deficient CDG patient. Likewise, the integrity of the COG complex is also impaired in Cog1‐, Cog4‐ and Cog6‐depleted cells. Significantly, deficiency of Cog1, Cog4, Cog6 or Cog8 distinctly influences the production of COG subcomplexes and their Golgi targeting. These results shed light on the structural organization of the COG complex and its subcellular localization, and suggest that its integrity is required for both tethering of transport vesicles to the Golgi apparatus and the assembly of Golgi SNARE complexes. We propose that these two key functions are generally and mechanistically impaired in COG‐associated CDG patients, thereby exerting severe pleiotropic defects.     

Computational structure characterisation tools in application to ordered and disordered porous materials

In this article, we present a set of computational tools for systematic characterisation of ordered and disordered porous materials. These tools include calculation of the accessible surface area and geometric pore size distribution, analysis of the structure connectivity and percolation analysis of the porous space. We briefly discuss the algorithms behind these calculations. To demonstrate the capabilities of the tools and the type of insights that can be gained from their application, we consider a series of case studies. These case studies include small molecular fragments, several crystalline metal-organic materials, and variants of these materials with induced defects and disorder in their structure. The simulation package is available upon request.