Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

Background  

Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos.     

Basolateral K channels in an insect epithelium. Channel density, conductance, and block by barium

K channels in the basolateral membrane of insect hindgut were studied using current fluctuation analysis and microelectrodes. Locust recta were mounted in Ussing-type chambers containing Cl-free saline and cyclic AMP (cAMP). A transepithelial K current was induced by raising serosal [K] under short-circuit conditions. Adding Ba to the mucosal (luminal) side under these conditions had no effect; however, serosal Ba reversibly inhibited the short-circuit current (Isc), increased transepithelial resistance (Rt), and added a Lorentzian component to power density spectra of the Isc. A nonlinear relationship between corner frequency and serosal [Ba] was observed, which suggests that the rate constant for Ba association with basolateral channels increased as [Ba] was elevated. Microelectrode experiments revealed that the basolateral membrane hyperpolarized when Ba was added: this change in membrane potential could explain the nonlinearity of the 2 pi fc vs. [Ba] relationship if external Ba sensed about three-quarters of the basolateral membrane field. Conventional microelectrodes were used to determine the correspondence between transepithelially measured current noise and basolateral membrane conductance fluctuations, and ion-sensitive microelectrodes were used to measure intracellular K activity (acK). From the relationship between the net electrochemical potential for K across the basolateral membrane and the single channel current calculated from noise analysis, we estimate that the conductance of basolateral K channels is approximately 60 pS, and that there are approximately 180 million channels per square centimeter of tissue area.     

Isolated persistent hypermethioninemia.

New information has been obtained on 30 patients with isolated persistent hypermethioninemia, most of them previously unreported. Biopsies to confirm the presumptive diagnosis of partially deficient activity of ATP: L-methionine S-adenosyltransferase (MAT; E.C.2.5.1.6) in liver were not performed on most of these patients. However, none showed the clinical findings or the extreme elevations of serum folate previously described in other patients with isolated hypermethioninemia considered not to have hepatic MAT deficiency. Patients ascertained on biochemical grounds had no neurological abnormalities, and 27/30 had IQs or Bayley development-index scores within normal limits or were judged to have normal mental development. Methionine transamination metabolites accumulated abnormally only when plasma methionine concentrations exceeded 300-350 microM and did so more markedly after 0.9 years of age. Data were obtained on urinary organic acids as well as plasma creatinine concentrations. Patterns of inheritance of isolated hypermethioninemia were variable. Considerations as to the optimal management of this group of patients are discussed.     

Dog kidney (Na+,K+)-ATPase is more sensitive to inhibition by vanadate than human red cell (Na+,K+)-ATPase

(Na+,K+)-ATPase (EC 3.6.1.3) from kidney is more sensitive to inhibition by vanadate than red cell (Na+,K+)-ATPase. The difference appears to be in the apparent affinities of the two enzymes for K+ and Na+ at sites where K+ promotes and Na+ opposes vanadate binding. As a result of Na+-K+ competition at these sites, reversal of vanadate inhibition was accomplished at lower Na+ concentrations in red cell than in kidney (NA+,K+)-ATPase. It is possible that vanadate could selectively regulate Na+ transport in the kidney.     

Preimplantation embryo development in the mouse: Role of histidine decarboxylase

The present study determines the effect of a specific and an irreversible inhibitor of histidine decarboxylase (HDC), α-fluoromethylhistidine (α-FMH) on the mouse preimplantation embryo development in vitro. The embryo culture technique was used to assess the effect of α-FMH. Embryos recovered at 0800–0900 hr (AM) on day 3 of pregnancy were 4–8 cells, whereas those recovered at 1600–1630 hr were mostly 8-cell compacted embryos. Of the day 3-AM embryos, 81.3 ± 4.3% developed to blastocysts within 48 hr when cultured in the medium alone, but addition of α-FMH (0.19 or 0.38 mM) drastically reduced the blastocyst formation to 26.6 ± 7 or 16.8 ± 4.3%. Most of them were arrested before the compaction stage. Addition of L-histidine, the substrate for HDC, did not alter the inhibition of blastocyst formation in the presence of α-FMH (37.2 ± 10.9%). Of the day 3-PM embryos, 99.3 ± 0.7% developed to blastocyst stage when cultured in the medium alone and addition of α-FMH (0.19 or 0.38 mM) did not affect the embryo development (92.1 ± 4.3 or 81.9 ± 9.9% developed to blastocysts). The birth of healthy young following transfer of these blastocysts into pseudopregnant mice indicates normal development of the embryos under this condition. The results suggest that histamine synthesis may be required for the process of compaction and thus the formation of blastocyst.     

Restriction-map variation with the yellow-achaete-scute region in five populations of Drosophila melanogaster

It has been proposed that the degree of recombination for a genomic region will affect the level of both nucleotide heterozygosity and the density of transposable elements. Both features of genomic diversity have been examined in a number of recent reports for regions undergoing relatively normal levels of recombination in Drosophila melanogaster. In this study the genomic variation associated with yellow-achaete- scute loci located at the tip of the X chromosome is examined by six- cutter restriction mapping. In this region, as usual for regions adjacent to telomeres, crossing-over is dramatically reduced, and published studies of visible mutants indicate extremely little restriction-map variation. Eight six-cutter restriction endonucleases were used to locate sequence variation in 14- and 16.5-kb regions in 109 lines sampled from North America, Africa, and Europe. The overall level of heterozygosity is estimated as 0.29%. Nine large insertions, all presumed to be transposable elements, were observed. Base-pair heterozygosity appears to be reduced compared with regions having normal levels of recombination. The estimated heterozygosity is much higher than reported in earlier studies of restriction-map variation among visible mutations in the complex. The incidence of large insertions is not elevated compared with that in other regions of the genome. This suggests that asymmetric synapsis and exchange is not an important mechanism for the elimination of transposable elements.      

Characterisation of<Emphasis Type="Italic">fusarium graminearum</Emphasis> and<Emphasis Type="Italic">F. culmorum</Emphasis> isolates by mycotoxin production and aggressiveness to wheat

A total of 27Fusarium culmorum isolates from Germany and 41F. graminearum isolates from Kenya were investigated for aggressiveness and mycotoxin production on wheat ears. In addition, ergosterol content of the kernels from ears inoculated withF. graminearum was determined and theF. culmorum isolates were tested for mycotoxin productionin vitro. For both pathogens, isolates markedly differed in aggressiveness. 59% and 37% of theF. culmorum isolates produced NIV and DON, respectively,in vivo andin vitro. The DON-producing isolates also produced 3-acDONin vitro. The more aggressive isolates produced mainly DON while the less aggressive isolates produced mainly NIV. 12% and 85% of theF. graminearum isolates produced NIV and DON, respectively. The highly aggressive isolates produced higher amounts of DON, aggressiveness being highly correlated to DON content in the kernels. NIV-producing isolates were less aggressive. Ergosterol content of kernels was moderately correlated to aggressiveness but highly correlated to DON content. Disease severity was associated with kernel weight reduction.