The alpha-operon equivalent genome region in the extreme halophilic archaebacterium Haloarcula (Halobacterium) marismortui.

The genome region of the extreme halophilic archaebacterium Haloarcula marismortui equivalent to the alpha-operon of Escherichia coli has been characterized. In H. marismortui, the alpha-operon was found to be located immediately upstream from the S9 gene cluster. The gene order in the halobacterial alpha-operon, given according to the gene products, is tRNA(Ser), HmaS13, HmaS4, HmaS11, and HmaRp alpha. Compared to the corresponding operon from E. coli, the halobacterial gene organization differs in (i) the presence of a gene for tRNA(Ser) (GCU), (ii) the reversed order of the genes for the ribosomal proteins HmaS11 and HmaS4, and (iii) the absence of the gene coding for the ribosomal protein L17. The primary structure of HmaRp alpha shows high similarity to a subunit of eukaryotic RNA polymerase II (YeaRpB3, HsaRpB33), whereas the similarity to the eubacterial alpha-subunit of RNA polymerase is only weak.     

Roll Compaction and Tableting of High Loaded Metformin Formulations Using Efficient Binders

Metformin has a poor tabletability and flowability. Therefore, metformin is typically wet granulated with a binder before tableting. To save production costs, it would be desirable to implement a roll compaction/dry granulation (RCDG) process for metformin instead of using wet granulation. In order to implement RCDG, the efficiency of dry binders is crucial to ensure a high drug load and suitable properties of dry granules and tablets. This study evaluates dry granules manufactured by RCDG and subsequently tableting of high metformin content formulations (≥?87.5%). Based on previous results, fine particle grades of hydroxypropylcellulose and copovidone in different fractions were compared as dry binders. The formulations are suitable for RCDG and tableting. Furthermore, results can be connected to in-die and out-of-die compressibility analysis. The addition of 7% of dry binder is a good compromise to generate sufficient mechanical properties on the one hand, but also to save resources and ensure a high metformin content on the other hand. Hydroxypropylcellulose was more efficient in terms of granule size, tensile strength and friability. Three percent croscarmellose was added to reach the specifications of the US Pharmacopeia regarding dissolution. The final formulation has a metformin content of 87.5%. A loss in tabletability does not occur for granules compressed at different specific compaction forces, which displays a robust tensile strength of tablets independent of the granulation process.     

A comparative analysis between SNPs and SSRs to investigate genetic variation in a juniper species (<Emphasis Type="Italic">Juniperus phoenicea</Emphasis> ssp. <Emphasis Type="Italic">turbinata</Emphasis>)

Genomic resources are a valuable research tool for understanding and forecasting the response of forest trees to global change and for developing science-based management strategies. Yet, many ecologically relevant tree species still lack such resources. The conifer genus Juniperus contains >?70 species that are widely distributed through the Northern Hemisphere, including several keystone species that form extensive forests in arid landscapes. To date, single-nucleotide polymorphism (SNP) markers have not been described for this ecologically important tree genus and the few described simple sequence repeat (SSR) markers result insufficient for performing reliable population demographic inference. Here, we report on the successful development of 19 new SSR and 147 SNP markers for Phoenician juniper (Juniperus phoenicea ssp. turbinata), a species widely distributed along the coasts of the Mediterranean Basin. We calculate a series of population genetic diversity estimates for each set of markers independently and for both sets combined. Our comparison shows that the higher per-locus information content of SSRs makes them the marker of choice for parentage and assignment studies, whereas SNPs provide more reliable demographic inferences (N_e and detection of a recent bottleneck). We also test and confirm the transferability of the new set of SNP markers to the closely related tetraploid species J. thurifera. Finally, we perform an orthology analysis with two gymnosperm model species to search for SNPs linked with functional genes.     

Rapid and reliable protein structure determination via chemical shift threading

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often?<?10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)—with an average TM-score performance of 0.68 (vs. 0.50–0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca.     

Effect of Separation Conditions on Automated Isoelectric Focusing of Carbohydrate-Deficient Transferrin and Other Human Isotransferrins Using the PhastSystem

To investigate the effect of automated isoelectric focusing conditions in the PhastSystem, e.g., the point of sample application, prerun and separation times, and minimized gels on isotransferrin band pattern, human sera were analyzed with native transferrin iron load, after iron saturation or iron depletion in vitro. Varying the focusing conditions we found (i) Point of sample application (anode, middle of the gel, cathode) strongly affected transferrin iron loss. It was greatest at the anode and least at the cathode. (ii) Without prerun, distinct transferrin iron loss also occurred. A short prerun time prevented iron loss, but increasing it did not improve transferrin iron load stability as stated by others. (iii) An inappropriately long separation time inevitably yielded iron loss. In conclusion, inappropriate isoelectric focusing conditions strongly affect iron load stability of isotransferrins (obviously via low pH within the gel), resulting in transferrin iron release and cofocusing of isotransferrins with different sialic acid or iron contents. For determination of carbohydrate-deficient transferrin, such conditions resulted in overestimation of the marker of chronic alcohol abuse. Our findings may be of guiding importance for isoelectric focusing of protein-ligand complexes. We recommend the procedure described for development of isoelectric focusing of protein-ligand complexes.     

Estimation of protein digestibility—IV. Digestive proteinases from the pyloric caeca of coho salmon (Oncorhynchus kisutch) fed diets containing soybean meal

The goal of this study was to better understand why dietary soybean products are poorly utilized by salmonids. The influence of dietary intake on coho salmon fingerling weight gain and specific properties of pyloric caeca enzymes was investigated. Fingerlings were fed diets containing heated or unheated soybean meal (SBM) or Promoveal™, as 15–25% herring meal replacer, for 8–12 weeks. Fish fed to apparent satiation with diets containing heated SBM replacer gained more weight than those fed unheated SBM at the same level. Fish increased in body weight at the same rate when fed restricted rations containing either 15% SBM replacer that was variously heated up to 20 min, 15% Promoveal™ replacer or the herring meal basal diet. After the experimental diets were fed, digestive proteinases were isolated from the pyloric caeca. Yield of pyloric caeca enzymes (PCE), recovery of trypsin in PCE, soybean trypsin inhibitor (SBTI) sensitivity of PCE trypsin, specific activity of PCE trypsin and in vitro casein digestibility by PCE were determined for each dietary group. Weight gain vs in vitro casein digestibility by PCE was linear for animals fed unheated SBM to apparent satiation (r² = 0.71, P < 0.1) but not for animals fed either heated SBM to apparent satiation or variously heated SBM as 15% replacer at restricted levels. Trypsin from fish fed diets with heated or unheated SBM, but not Promoveal™ replacer, was less sensitive to SBTI than fish fed no SBM. For fish fed diets with variously heated SBM as 15% replacer, the SBTI activity of the SBM and SBTI inhibition of PCE trypsin were inversely related (r² = 0.88, P < 0.05). The yield of PCE was higher for fish fed 25% of heated SBM replacer than it was for diet groups fed less SBM. The yield of PCE trypsin was higher from animals fed 25% heated SBM replacer than those fed diets with a lower percentage of heated SBM replacer. Feeding coho fingerlings rations with SBM replacer appears to promote physiological compensation of PCE. Heat stable and/or heat-activated factor(s) and SBTI appear to cause the compensation of salmon digestive proteinases from coho salmon fed diets with SBM.