Increased isoleucine acceptance by sulfur-deficient transfer RNA from Escherichia coli.

Sulfur-deficient tRNA, isolated from Escherichia coli HfrC, rel-, met-, cys-, lambda, after cysteine starvation, was found to have an increased acceptance of isoleucine in proportion to the deficiency of 4-thiouridine. Isoleucine acceptance was not altered in the presence of other amino acids of CTP, and the higher acceptance was observed over a wide range of magnesium, isoleucine, tRNA and enzyme concentrations. The Vmax value for sulfur-deficient tRNA was more than three times greater than observed for normal tRNA. Methylated albumin kieselguhr (MAK) chromatography revealed three isoacceptor peak for normal tRNA, while sulfur-deficient tRNA was missing tRNAile, and exhibited a larger, shifted peaks for tRNA normal tRNA, while sulfur-deficient tRNA was missing tRNAille 2, and exhibited a large shifted peak for tRNAile 3 . Treatment with crude RNA sulfurtransferase both lowered the isoleucine acceptance for sulfur-deficient tRNA to that seen for normal tRNA, and restored the missing isoacceptor on MAK. The possibility that thionucleotides may play a role in the aminoacylation of tRNAile in E. coli is discussed.     

Evolutionarily conserved motifs and modules in mitochondrial protein–protein interaction networks

Advances in organelle interactomics have led to new insights into organelle functions. In this study, we considered the common mitochondrial PIN of four evolutionarily distant eukaryotic species, namely Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. By comparative interactomics analysis of mitochondrial PINs in these organisms, five conserved modules were identified. Modules comprise the main mitochondrial tasks, including proteins involved in translation process, mitochondrial import inner membrane proteins, TCA cycle enzymes, mitochondrial electron transport chain, and metabolic enzymes. Furthermore, we reemphasize that subgraphs of network, i.e., motifs and themes, may represent evolutionarily conserved topological units which are biologically significant.     

Adaptive neuro-fuzzy inference system: Estimation of soil aggregates stability

In present study, the capabilities of multiple linear regression (MLR) and adaptive neuro-fuzzy inference system (ANFIS) in developing pedotransfer functions (PTFs) for estimating geometric mean diameter (GMD) and mean weight diameter (MWD), from routine soil properties and combination of routine soil properties and fractal dimension of aggregates were evaluated. For this reason 101 samples were collected form the Northwest of Iran and some their properties such as soil texture, pH, cation exchange capacity (CEC), and organic matter (OM), fractal dimension of aggregates between number-diameter (Dn), mass-diameter (Dmt), and bulk density-diameter (Dmy) were determined and used as an input variables for determining of mean weight diameter (MWD) and geometric mean diameter (GMD) by MLR and ANFIS PTFs. Results showed that the application of fractal dimension of aggregates as a predictor in two methods improved the accuracy of PTFs. As well as, results showed that ANFIS have greater potential for determination of the relationships between soil aggregate stability indices and other soil properties in compared with MLR. Therefore using of adaptive neuro-fuzzy inference system (ANFIS) in developing pedotransfer functions is recommended.     

Analysis of Metabolic Subnetworks by Flux Cone Projection

Background

Analysis of elementary modes (EMs) is proven to be a powerful constraint-based method in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their large number, EMs cannot be simply used as an input for subsequent analysis. One possibility is to limit the analysis to a subset of interesting reactions. However, analysing an isolated subnetwork can result in finding incorrect EMs which are not part of any steady-state flux distribution of the original network. The ideal set to describe the reaction activity in a subnetwork would be the set of all EMs projected to the reactions of interest. Recently, the concept of "elementary flux patterns" (EFPs) has been proposed. Each EFP is a subset of the support (i.e., non-zero elements) of at least one EM.

Results

We introduce the concept of ProCEMs (Projected Cone Elementary Modes). The ProCEM set can be computed by projecting the flux cone onto a lower-dimensional subspace and enumerating the extreme rays of the projected cone. In contrast to EFPs, ProCEMs are not merely a set of reactions, but projected EMs. We additionally prove that the set of EFPs is included in the set of ProCEM supports. Finally, ProCEMs and EFPs are compared for studying substructures of biological networks.

Conclusions

We introduce the concept of ProCEMs and recommend its use for the analysis of substructures of metabolic networks for which the set of EMs cannot be computed.     

Efficient distinction of invasive aquatic plant species from non‐invasive related species using DNA barcoding

Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non‐invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH‐psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH‐psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics.     

The Bruce effect in Norway rats

Intrauterine implantation of fertilized ova can be blocked by exposing recently inseminated females with an unfamiliar male. This selective pregnancy failure, designated as the Bruce effect (Bruce, Nature 1959; 184:105), is well studied in laboratory mice and has been confirmed in several other rodent species. However, no clear information exists concerning this phenomenon in the laboratory rat. The present study was conducted to investigate whether or not the Bruce effect exists in the rat. Females of two F1 hybrid strains (n(total) = 354) with different MHC genotypes (F344BNF1, RT1(lv1/n), and LEWPVGF1, RT1(l/c)) were mated with males of their own strain and subsequently exposed during the first 4 days postcoitus either to a male of the other hybrid strain or to an unfamiliar male of the same strain as the stud. The litter rate of each treatment group was determined. As a control, mated females of both strains were reexposed to the stud male to determine baseline litter rates. Female rats of both F1 hybrid strains showed a significantly lower litter rate when exposed to males of a different strain than their stud male, compared to the expected values of birth rates observed in control females (F344BNF1: P = 0.017; LEWPVGF1: P = 0.019). In contrast, there was no difference between expected and observed litter rates in females of both F1 hybrid strains after exposure to an unfamiliar male of the same strain as their stud. Our results demonstrate for the first time that the Bruce effect, well documented in mice, occurs in the Norway rat.     

Human histone genes are interspersed with members of the Alu family and with other transcribed sequences

We have isolated a series of recombinant λCh4A phages containing human histone genes. Histone H2A, H2B, H3 and H4 genes have been found to be clustered, but are not present in any simple repeat pattern. Hybridization of a blot containing phage DNA with S phase polysomal cDNA indicates the presence of additional sequences complementary to HeLa polysomal RNA sequences. Northern blot analysis using these clones as probes has also shown the presence of sequences complementary to non-histone-coding RNAs, some of which accumulate differentially in different stages of the cell cycle. We have also found, by hybridization with appropriate probes, that histone genes are interspersed with several copies of the Alu DNA family; however, not all of the histone genes are associated with an Alu DNA sequence.