Specific association of iduronic acid-rich dermatan sulphate with the extracellular matrix of human skin fibroblasts cultured on collagen gels.

Human skin fibroblasts cultured on collagen gels produced two dermatan sulphate species, one, enriched in iduronic acid residues, that bound specifically to the collagenous fibres of the gel, the other, enriched in glucuronic acid, that accumulated in the culture medium. Collagen-binding and collagen-non-binding dermatan sulphates were also produced by cells grown on plastic surfaces, but in these cultures each constituent was released into the growth medium. Net synthesis of dermatan sulphate was 3-fold higher in cells maintained on collagen gels. In contrast, heparan sulphate synthesis was not influenced by the nature of the culture surface. The concentration of heparan sulphate in surface-membrane extracts was similar for cells grown on plastic and on collagen gels, but cells cultured on collagen showed a notable increase in the content of surface-membrane dermatan sulphate. The patterns of synthesis and distribution of sulphated glycosaminoglycans observed in skin fibroblasts maintained on collagen gels may reflect differentiated cellular functions.     

Changes in body size of newborns in Lithuania, 1974-2004

The purpose of this study was to analyse body size of Lithuanian newborns born in 1998 and 2004, and to compare results with the data from 1974. The main body size measurements - body weight, body length and body mass index (BMI) of 3281 (1705 boys and 1576 girls) live term singleton Lithuanian newborns' were analysed according to gestational age, sex and health status. The data were collected in the Clinic of Obstetrics and Gynaecology of Vilnius University (VU COG), and the comparison with the data of Lithuanian Medical Birth Register of (LMBR) was performed. No significant differences between height, weight and body mass index in 1998 and the same characteristics in 2004 were observed. Means and principal percentiles (10th, 50th, 90th) of body measurements of 37-42 weeks of gestational age newborns were obtained. The mean body length was 52.8/52.19 cm (boys/girls), body weight--3589/3454 g, BMI 12.82/12.64 correspondingly. The recent data were compared with the similar data from 1974 cohort. Statistically significant increment of body length of Lithuanian newborns was observed in all age and sex groups, whereas weight changes were less evident. The analysis of BMI demonstrated the following trend: newborns became longer, but not relatively heavier in comparison with the similar data 30 years ago. Hence, it is important to evaluate weight changes of neonate in relation with the changes in height. Further investigation of prevalence of neonatal macrosomia, possible factors of body size changes, their relationship to general health status and further health issues of the child should be explored.     

Domain-specific modification of heparan sulfate by Qsulf1 modulates the binding of the bone morphogenetic protein antagonist Noggin

We have reported previously that Noggin is a heparin-binding protein and associates with the cell surface through heparan sulfate proteoglycans, where it remains functional for the binding of bone morphogenetic proteins (BMPs). Here we report that the binding of Noggin to the cell surface is highly selective for heparan sulfate and that specific structural features are required for the interaction. Noggin binds most efficiently to heparin sequences composed of 10 or more monosaccharides; N-, 6-O-, and 2-O-sulfates contribute to this interaction. In addition, we have shown that the developmentally regulated endosulfatase Qsulf1 selectively removes sulfate groups from the 6-O position of sugars within the most highly sulfated S domains of heparan sulfate, whereas 6-O-sulfates in the NA/NS domains are not substrates for the enzyme. The activity of Qsulf1 in cells in culture results in the release of Noggin from the cell surface and a restoration of BMP responsiveness to the cells. This shows that Noggin binds to the S domains of heparan sulfate and provides evidence that, in addition to modulating Wnt signaling in vivo by the release of heparan sulfate bound Wnt, Qsulf1 also modulates BMP signaling by the release of surface-bound Noggin.     

Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family

The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes involved in DNA repair and recombination. Many of the GIY-YIG family enzymes are functional as monomers. We show here that the Cfr42I restriction endonuclease which belongs to the GIY-YIG family and recognizes the symmetric sequence 5′-CCGC/GG-3′ (‘/’ indicates the cleavage site) is a tetramer in solution. Moreover, biochemical and kinetic studies provided here demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous binding of two copies of its recognition sequence. In that respect Cfr42I resembles the homotetrameric Type IIF restriction enzymes that belong to the distinct PD-(E/D)XK nuclease superfamily. Unlike the PD-(E/D)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an extremely wide selection of metal-ion cofactors, including Mg²⁺, Mn²⁺, Co²⁺, Zn²⁺, Ni²⁺, Cu²⁺ and Ca²⁺. To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme. Similar structural arrangement and phenotypes displayed by restriction enzymes of the PD-(E/D)XK and GIY-YIG nuclease families point to the functional significance of tetramerization.     

Effects of the loss of clonal integration on four sedges that differ in ramet aggregation

Although clonal growth is a dominant mode of plant growth in wetlands, the importance of clonal integration, resource sharing among ramets, to individual ramet generations (mother and daughter) and entire clones of coexisting species has not been well investigated. This study evaluated the significance of clonal integration in four sedge species of varying ramet aggregations, from clump-forming species (Clumpers –Carex sterilis, Eleocharis rostellata), with tightly aggregated ramets (rhizomes<1cm), to runner species (Runners –Schoenoplectus acutus, Cladium mariscoides), with loosely aggregated ramets. We manipulated clonal integration by either severing connections between target mother and daughter ramets or leaving connections intact, and then planted them in an intact neighborhood of a fen in Michigan, USA. We measured growth parameters of original and newly produced ramets over two growing seasons and conducted a final biomass harvest, to address four hypotheses. First, we expected integrated clones to accumulate more biomass than severed clones. However, final clone-level biomass and ramet production were the same for both treatments in all species although severing initially stimulated ramet production by Schoenoplectus and produced a more compact ramet aggregation in Cladium. Second, we hypothesized that mother ramets would experience a cost of integration, through reduced ramet or biomass production, while daughters would experience a benefit, through increased resource availability from mothers. Mother ramets of Cladium suffered a cost from integration, while Schoenoplectus mothers suffered a slight cost and Carex daughters saw a slight benefit. Finally, we hypothesized that integration would be more active in runner species than in clumper species. Indeed, we documented more active integration in runners than clumpers, but none of the study species were dependent upon integration for growth or survival once daughter ramets were established with their own roots and shoots. This study demonstrates that integration between established ramets may not be the most important advantage to clonal growth in this wetland field site. The loss of integration elicited varied responses among coexisting species in their natural habitat, somewhat but not completely related to their growth form, suggesting that a combination of plant life history traits contributes to the dependence upon clonal integration among established ramets of clonal species.     

Cattle cDNA clones encoding MHC class II DQB1 and DQB2 genes

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers D37952, D37953, and D37954     

Design of a CRISPR-Cas system to increase resistance of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> to bacteriophage SPP1

Clustered regularly interspaced short palindromic repeats (CRISPR) together with CRISPR-associated (cas) genes form an adaptive prokaryotic immune system which provides acquired resistance against viruses and plasmids. Bacillus subtilis presently is the best-characterized laboratory model for Gram-positive bacteria and also widely used for industrial production of enzymes, vitamins and antibiotics. In this study, we show that type II-A CRISPR-Cas system from Streptococcus thermophilus can be transferred into B. subtilis and provides heterologous protection against phage infection. We engineered a heterologous host by cloning S. thermophilus Cas9 and a spacer targeting bacteriophage SPP1 into the chromosome of B. subtilis, which does not harbor its own CRISPR-Cas systems. We found that the heterologous CRISPR-Cas system is functionally active in B. subtilis and provides resistance against bacteriophage SPP1 infection. The high efficiency of the acquired immunity against phage could be useful in generation of biotechnologically important B. subtilis strains with engineered chromosomes.     

Glycosaminoglycans inhibit the adherence and the spreading of osteoclasts and their precursors: role in osteoclastogenesis and bone resorption

The bone microenvironment (e.g. glycosaminoglycans (GAGs), growth factors) plays a major role in bone resorption, especially in the formation of osteoclasts which differentiate from the hematopoietic lineage in the presence of RANKL. Previous studies revealed that GAGs may influence osteoclastogenesis, but data are very controversial, some studies showing an inhibitory effect of GAGs on osteoclastic differentiation whereas others demonstrated a stimulatory effect. To clarify their activities, we investigated the effect of 5 families of GAGs in three different models of human/mouse osteoclastogenesis. The present data revealed that heparin inhibited osteoclastogenesis in these three models, which was confirmed by a decrease in mRNA expression of osteoclastic markers and by an inhibition of the bone resorption capacity. We also demonstrated in RAW 264.7 cells that other families of GAGs different from heparin inhibited RANKL-induced osteoclastogenesis, and that this inhibition was dependent on the length and the level of sulfation of GAGs. In the present work, heparin did not bind to RANKL and did not modulate RANKL signaling. Heparin acted at 2 distinct steps of osteoclastogenesis from human CD14(+) cells: first, heparin strongly decreased the adherence of osteoclast precursors, and secondly inhibited osteoclasts to spread and to be active. Furthermore, the second action of heparin was reversible as the removal of heparin at the end of the culture time allowed the condensed cells to spread out and showed the formation of morphological active osteoclasts. The present work clearly evidences that GAGs inhibit osteoclastogenesis in vitro and strengthens the therapeutic interest of defined GAGs in osteolytic diseases.     

In vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus

Clustered regularly interspaced short palindromic repeats (CRISPR)‐encoded immunity in Type I systems relies on the Cascade (CRISPR‐associated complex for antiviral defence) ribonucleoprotein complex, which triggers foreign DNA degradation by an accessory Cas3 protein. To establish the mechanism for adaptive immunity provided by the Streptococcus thermophilus CRISPR4‐Cas (CRISPR‐associated) system (St‐CRISPR4‐Cas), we isolated an effector complex (St‐Cascade) containing 61‐nucleotide CRISPR RNA (crRNA). We show that St‐Cascade, guided by crRNA, binds in vitro to a matching proto‐spacer if a proto‐spacer adjacent motif (PAM) is present. Surprisingly, the PAM sequence determined from binding analysis is promiscuous and limited to a single nucleotide (A or T) immediately upstream (?1 position) of the proto‐spacer. In the presence of a correct PAM, St‐Cascade binding to the target DNA generates an R‐loop that serves as a landing site for the Cas3 ATPase/nuclease. We show that Cas3 binding to the displaced strand in the R‐loop triggers DNA cleavage, and if ATP is present, Cas3 further degrades DNA in a unidirectional manner. These findings establish a molecular basis for CRISPR immunity in St‐CRISPR4‐Cas and other Type I systems.