GenePath: a system for automated construction of genetic networks from mutant data

MOTIVATION: Genetic networks are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. RESULTS: We have developed GenePath, an intelligent assistant that automates the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints in the search for a plausible genetic network. GenePath formalizes genetic data analysis, facilitates the consideration of all the available data in a consistent manner, and the examination of the large number of possible consequences of planned experiments. It also provides an explanation mechanism that traces every finding to the pertinent data. AVAILABILITY: GenePath can be accessed at http://genepath.org. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://genepath.org/bi-.supp.     

The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold

The G-rich 11-mer oligonucleotide d(G(4)T(4)G(3)) forms a bimolecular G-quadruplex in the presence of sodium ions with a topology that is distinct from the folds of the closely related and well-characterized sequences d(G(4)T(4)G(4)) and d(G(3)T(4)G(3)). The solution structure of d(G(4)T(4)G(3))(2) has been determined using a combination of NMR spectroscopy and restrained molecular dynamics calculations. d(G(4)T(4)G(3))(2) forms an asymmetric dimeric fold-back structure consisting of three stacked G-quartets. The two T(4) loops that span diagonally across the outer faces of the G-quartets assume different conformations. The glycosidic torsion angle conformations of the guanine bases are 5'-syn-anti-syn-anti-(T(4) loop)-anti-syn-anti in one strand and 5'-syn-anti-syn-anti-(T(4) loop)-syn-anti-syn in the other strand. The guanine bases of the two outer G-quartets exhibit a clockwise donor-acceptor hydrogen-bonding directionality, while those of the middle G-quartet exhibit the anti-clockwise directionality. The topology of this G-quadruplex, like other bimolecular fold-back structures with diagonal loops, places each strand of the G-quartet region next to a neighboring parallel and an anti-parallel strand. The two guanine residues not involved in G-quartet formation, G4 and G12 (i.e. the fourth guanine base of one strand and the first guanine base of the other strand), adopt distinct conformations. G4 is stacked on top of an adjacent G-quartet, and this base-stacking continues along with the bases of the loop residues T5 and T6. G12 is orientated away from the core of G-quartets; stacked on the T7 base and apparently involved in hydrogen-bonding interactions with the phosphodiester group of this same residue. The cation-dependent folding of the d(G(4)T(4)G(3))(2) quadruplex structure is distinct from that observed for similar sequences. While both d(G(4)T(4)G(4)) and d(G(3)T(4)G(3)) form bimolecular, diagonally looped G-quadruplex structures in the presence of Na(+), K(+) and NH(4)(+), we have observed this folding to be favored for d(G(4)T(4)G(3)) in the presence of Na(+), but not in the presence of K(+) or NH(4)(+). The structure of d(G(4)T(4)G(3))(2) exhibits a "slipped-loop" element that is similar to what has been proposed for structural intermediates in the folding pathway of some G-quadruplexes, and therefore provides support for the feasibility of these proposed transient structures in G-quadruplex formation.     

Vibratory signals of the harlequin bug and their transmission through plants

Abstract. Males of the harlequin bug, Murgantia histrionica (Hahn), produce five different vibrational songs, whereas females produce one song. Songs differ from those of other stink bugs primarily in their species‐specific temporal characteristics. The broad band male courtship songs of M. histrionica are achieved by a combination of different frequency modulated and/or narrow band subunits, with several higher harmonic frequencies. Males rather than females initiate substrate‐borne vibrational communication, and the longer‐range calling songs found typically in other pentatomid species are lacking. Interindividual differences in song temporal and spectral characteristics are discussed. Transmission of vibrational songs through a cabbage head is more efficient along veins than along lamina. Attenuation of signals transmitted through veins is low and similar to that reported previously for plant stalks. On the leaf vein, distances between peak amplitude minima and maxima are different for the dominant and subdominant frequencies. At any distance from the vibration source, a different relationship between spectral peak amplitudes can be recorded. Resolution of these differences, together with velocity differences between signals recorded on the vein and lamina, may help small stink bugs to estimate distance and to locate each other on a plant.     

NMR Study on The Tuning of North ⇆ South Equilibrium in Nucleos(t)ides by Metal Ion Interactions

Abstract

The NMR study on the interactions of dGpMe (1), MepdG (2) and dG (3) with Mg²⁺, Zn²⁺ and Hg²⁺ ions in D₂O solution has shown that binding of softer metal ions to N7 shifts N ? S pseudorotational equilibrium towards N-type conformations. At the same time the population of the anti conformers is slightly increased.     

Targeted high-throughput sequencing identifies mutations in atlastin-1 as a cause of hereditary sensory neuropathy type I

Hereditary sensory neuropathy type I (HSN I) is an axonal form of autosomal-dominant hereditary motor and sensory neuropathy distinguished by prominent sensory loss that leads to painless injuries. Unrecognized, these can result in delayed wound healing and osteomyelitis, necessitating distal amputations. To elucidate the genetic basis of an HSN I subtype in a family in which mutations in the few known HSN I genes had been excluded, we employed massive parallel exon sequencing of the 14.3 Mb disease interval on chromosome 14q. We detected a missense mutation (c.1065C>A, p.Asn355Lys) in atlastin-1 (ATL1), a gene that is known to be mutated in early-onset hereditary spastic paraplegia SPG3A and that encodes the large dynamin-related GTPase atlastin-1. The mutant protein exhibited reduced GTPase activity and prominently disrupted ER network morphology when expressed in COS7 cells, strongly supporting pathogenicity. An expanded screen in 115 additional HSN I patients identified two further dominant ATL1 mutations (c.196G>C [p.Glu66Gln] and c.976 delG [p.Val326TrpfsX8]). This study highlights an unexpected major role for atlastin-1 in the function of sensory neurons and identifies HSN I and SPG3A as allelic disorders.     

The membrane lateral domain approach in the studies of lipid–protein interaction of GPI-anchored bovine erythrocyte acetylcholinesterase

A novel membrane lateral domain approach was used to test whether the activity of the membrane-bound enzyme acetylcholinesterase (AChE) depends on the local properties (e.g. local lipid ordering) of bovine erythrocyte-ghost membrane. This issue has an additional aspect of interest due to an alternative mode of insertion of AChE molecules into the membrane by the glycosylphosphatidylinositol (GPI) anchor. In our experiments the lateral domain membrane structure was influenced by temperature and by the addition of n-butanol, and was quantitatively characterized using the method of EPR spectrum decomposition. The activity of AChE was determined by a colorimetric assay in the same samples. The results show that the membrane stabilizes the conformation of the membrane-bound AChE compared to the isolated AChE. In addition, a correlation was observed between the temperature dependence of order parameter of the most-ordered domain type and the activity of AChE. Therefore, our findings support the idea that the function of GPI proteins can be modulated by the lipid bilayer. Based on the assumption that the overall activity of AChE depends on the order parameters of particular domain types as well as their proportions, two models for AChE activity were introduced. In the first, a random distribution of enzyme molecules was proposed, and in the second, localization of enzyme molecules in a single (cholesterol-rich) domain type was assumed. Better agreement between measured and calculated activity values speaks in favor of the second model.Abbreviations AChE Acetylcholinesterase - ATCI Acetylthiocholine iodide - DTNB 5,5-Dithio-bis(2-nitrobenzoic acid) - EPR Electron paramagnetic resonance - GPI Glycosylphosphatidylinositol - PBS Phosphate buffer saline     

Prokaryotic and Eukaryotic Airborne Microorganisms as Tracers of Microclimatic Changes in the Underground (Postojna Cave, Slovenia)

Bioaerosols in cave air can serve as natural tracers and, together with physical parameters, give a detailed view of conditions in the cave atmosphere and responses to climatic changes. Airborne microbes in the Postojna Cave system indicated very dynamic atmospheric conditions, especially in the transitory seasonal periods between winter and summer. Physical parameters of cave atmosphere explained the highest variance in structure of microbial community in the winter and in the summer. The airborne microbial community is composed of different microbial groups with generally low abundances. At sites with elevated organic input, occasional high concentrations of bacteria and fungi can be expected of up to 1,000?colony-forming units/m(3) per individual group. The most abundant group of airborne amoebozoans were the mycetozoans. Along with movements of air masses, airborne algae also travel deep underground. In a cave passage with elevated radon concentration (up to 60?kBq/m(3)) airborne biota were less abundant; however, the concentration of DNA in the air was comparable to that in other parts of the cave. Due to seasonal natural air inflow, high concentrations of biological and inanimate particles are introduced underground. Sedimentation of airborne allochthonous material might represent an important and continuous source of organic material for cave fauna.     

c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry

Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (U^py) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with U^py and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.