Description of the novel perchlorate-reducing bacteria Dechlorobacter hydrogenophilus gen. nov., sp. nov. and Propionivibrio militaris, sp. nov.

Novel dissimilatory perchlorate-reducing bacteria (DPRB) were isolated from enrichments conducted under conditions different from those of all previously described DPRB. Strain LT-1T was enriched using medium buffered at pH 6.6 with 2-(N-morpholino)ethanesulfonic acid (MES) and had only 95% 16S rRNA gene identity with its closest relative, Azonexus caeni. Strain MPT was enriched in the cathodic chamber of a perchlorate-reducing bioelectrical reactor (BER) and together with an additional strain, CR (99% 16S rRNA gene identity), had 97% 16S rRNA gene identity with Propionivibrio limicola. The use of perchlorate and other electron acceptors distinguished strains MPT and CR from P. limicola physiologically. Strain LT-1T had differences in electron donor utilization and optimum growth temperatures from A. caeni. Strains LT-1T and MPT are the first DPRB to be described in the Betaproteobacteria outside of the Dechloromonas and Azospira genera. On the basis of phylogenetic and physiological features, strain LT-1T represents a novel genus in the Rhodocyclaceae; strain MPT represents a novel species within the genus Propionivibrio. The names Dechlorobacter hydrogenophilus gen. nov., sp. nov and Propionivibrio militaris sp. nov. are proposed

NM23 proteins: innocent bystanders or local energy boosters for CFTR?

NM23 proteins NDPK-A and -B bind to the cystic fibrosis (CF) protein CFTR in different ways from kinases such as PKA, CK2 and AMPK or linkers to cell calcium such as calmodulin and annexins. NDPK-A (not -B) interacts with CFTR through reciprocal AMPK binding/control, whereas NDPK-B (not -A) binds directly to CFTR. NDPK-B can activate G proteins without ligand-receptor coupling, so perhaps NDPK-B's binding influences energy supply local to a nucleotide-binding site (NBD1) needed for CFTR to function. Curiously, CFTR (ABC-C7) is a member of the ATP-binding cassette (ABC) protein family that does not obey 'clan rules'; CFTR channels anions and is not a pump, regulates disparate processes, is itself regulated by multiple means and is so pleiotropic that it acts as a hub that orchestrates calcium signaling through its consorts such as calmodulin/annexins. Furthermore, its multiple partners make CFTR dance to different tunes in different cellular and subcellular locations as it recycles from the plasma membrane to endosomes. CFTR function in airway apical membranes is inhibited by smoking which has been dubbed 'acquired CF'. CFTR alone among family members possesses a trap for other proteins that it unfurls as a 'fish-net' and which bears consensus phosphorylation sites for many protein kinases, with PKA being the most canonical. Recently, the site of CFTR's commonest mutation has been proposed as a knock-in mutant that alters allosteric control of kinase CK2 by log orders of activity towards calmodulin and other substrates after CFTR fragmentation. This link from CK2 to calmodulin that binds the R region invokes molecular paths that control lumen formation, which is incomplete in the tracheas of some CF-affected babies. Thus, we are poised to understand the many roles of NDPK-A and -B in CFTR function and, especially lumen formation, which is defective in the gut and lungs of many CF babies

Computer database "NEVI" on endangerment by melanoma

A database containing statistically meaningful numbers of carefully verified cases of nevi pigmentosi (in four categories: benign nevus, blue nevus, suspicious nevus, and malignant melanoma) is described. Various experiments of controlled data mining were performed in order to gain insight into the interpretation of the TDS (total dermatoscopic score) coefficient, which is broadly used in the initial classification of endangerment by melanoma tumours

Some problems of chemical reactions retrieval systems

The paper briefly discusses some organisational questions of distribution of chemical information over the computer network, emphasizing various tools available for chemical sciences, mainly: chemical reaction retrieval systems, systems for computer-assisted molecular modelling, then for computational chemistry, biocomputing, and information about human genes. From the above mentioned problems, the chemical reaction retrieval systems, like ORAC, REACCS, and SYNLIB are covered in detail. Additionally, the latest philosophy of searching reaction databases, represented by a family of tools from InfoChem GmbH (ChemReact41, CD-ROM-with over 2.5 min of reactions-and STS), are critically reviewed

A new algorithm for generation of decision trees

A new algorithm for development of quasi-optimal decision trees, based on the Bayes theorem, has been created and tested. The algorithm generates a decision tree on the basis of Bayesian belief networks, created prior to the formation of the decision tree. The efficiency of this new algorithm was compared with three other known algorithms used to develop decision trees. The data set used for the experiments was a set of cases of skin lesions, histopatolgically verified

An improved comparison of three rough set approaches to missing attribute values

In a previous paper three types of missing attribute values: lost values, attribute-concept values and "do not care" conditions were compared using six data sets. Since previous experimental results were affected by large variances due to conducting experiments on different versions of a given data set, we conducted new experiments, using the same pattern of missing attribute values for all three types of missing attribute values and for both certain and possible rules. Additionally, in our new experiments, the process of incremental replacing specified values by missing attribute values was terminated when entire rows of the data sets were full of missing attribute values. Finally, we created new, incomplete data sets by replacing the specified values starting from 5% of all attribute values, instead of 10% as in the previous experiments, with an increment of 5% instead of the previous increment of 10%. As a result, it is becoming more clear that the best approach to missing attribute values is based on lost values, with small difference between certain and possible rules, and that the worst approach is based on "do not care" conditions, certain rules. With our improved experimental setup it is also more clear that for a given data set the type of the missing attribute values should be selected individually