Automation of gene assignments to metabolic pathways using high-throughput expression data

Background  

Accurate assignment of genes to pathways is essential in order to understand the functional role of genes and to map the existing pathways in a given genome. Existing algorithms predict pathways by extrapolating experimental data in one organism to other organisms for which this data is not available. However, current systems classify all genes that belong to a specific EC family to all the pathways that contain the corresponding enzymatic reaction, and thus introduce ambiguity.     

Production and partial purification of membrane proteins using a liposome-supplemented wheat cell-free translation system

Background  

Recently, some groups have reported on cell-free synthesis of functional membrane proteins (MPs) in the presence of exogenous liposomes (liposomes). Previously, we reported synthesis of a functional AtPPT1 plant phosphate transporter that was associated with liposomes during translation. However, it is unclear whether or not lipid/MP complex formation is common to all types of MPs in the wheat cell-free system.     

Phosphate uptake and utilization by bacteria and algae

Bacterial uptake of inorganic phosphate (closely investigated in Escherichia coli) is maintained by two different uptake systems. One (Pst system) is P_i-repressible and used in situations of phosphorus deficiency. The other system (Pit system) is constitutive. The Pit system also takes part in the phosphate exchange process where orthophosphate is continuously exchanged between the cell and the surrounding medium.Algal uptake mechanisms are less known. The uptake capacity increases during starvation but no clearly defined transport systems have been described. Uptake capacity seems to be regulated by internal phosphorus pools, e.g., polyphosphates. In mixed algal and bacterial populations, bacteria generally seem to be more efficient in utilizing low phosphate concentrations. The second half of this paper discusses how bacteria and algae can share limiting amounts of phosphate provided that the bacteria have pronouncedly higher affinity for phosphate. Part of the solution to this problem may be that bacteria are energy-limited rather than phosphate-limited and dependent on algal organic exudates for their energy supply.The possible phosphate exchange mechanism so convincingly demonstrated in Escherichia coli is here suggested to play a key role for the flux of phosphorus between bacteria and algae. Such a mechanism can also be used to explain the rapid phosphate exchange between the particulate and the dissolved phase which always occurs in short-term ³²P-uptake experiments in lake waters.     

Application of a wide-range yeast vector (CoMed?) system to recombinant protein production in dimorphic Arxula adeninivorans, methylotrophic Hansenula polymorpha and other yeasts

Background  

Yeasts provide attractive expression platforms in combining ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. However, early restriction to a single yeast platform can result in costly and time-consuming failures. It is therefore advisable to assess several selected systems in parallel for the capability to produce a particular protein in desired amounts and quality. A suitable vector must contain a targeting sequence, a promoter element and a selection marker that function in all selected organisms. These criteria are fulfilled by a wide-range integrative yeast expression vector (CoMed™) system based on A. adeninivorans- and H. polymorpha-derived elements that can be introduced in a modular way.     

High prevalence of extrapyramidal signs and symptoms in a group of Italian dental technicians

Background  

Occupational and chronic exposure to solvents and metals is considered a possible risk factor for Parkinson's disease and essential tremor. While manufacturing dental prostheses, dental technicians are exposed to numerous chemicals that contain toxins known to affect the central nervous system, such as solvents (which contain n-hexane in particular) and metals (which contain mercury, iron, chromium, cobalt and nickel).     

The zebrafish prospero homolog prox1 is required for mechanosensory hair cell differentiation and functionality in the lateral line

Background  

The lateral line system in zebrafish is composed of a series of organs called neuromasts, which are distributed over the body surface. Neuromasts contain clusters of hair cells, surrounded by accessory cells.     

SING: Subgraph search In Non-homogeneous Graphs

Background  

Finding the subgraphs of a graph database that are isomorphic to a given query graph has practical applications in several fields, from cheminformatics to image understanding. Since subgraph isomorphism is a computationally hard problem, indexing techniques have been intensively exploited to speed up the process. Such systems filter out those graphs which cannot contain the query, and apply a subgraph isomorphism algorithm to each residual candidate graph. The applicability of such systems is limited to databases of small graphs, because their filtering power degrades on large graphs.     

A subgroup of plant aquaporins facilitate the bi-directional diffusion of As(OH)<Subscript>3</Subscript> and Sb(OH)<Subscript>3</Subscript>across membranes

Background  

Arsenic is a toxic and highly abundant metalloid that endangers human health through drinking water and the food chain. The most common forms of arsenic in the environment are arsenate (As(V)) and arsenite (As(III)). As(V) is a non-functional phosphate analog that enters the food chain via plant phosphate transporters. Inside cells, As(V) becomes reduced to As(III) for subsequent extrusion or compartmentation. Although much is known about As(III) transport and handling in microbes and mammals, the transport systems for As(III) have not yet been characterized in plants.     

Removing celiac disease-related gluten proteins from bread wheat while retaining technological properties: a study with Chinese Spring deletion lines

Background  

Gluten proteins can induce celiac disease (CD) in genetically susceptible individuals. In CD patients gluten-derived peptides are presented to the immune system, which leads to a CD4⁺ T-cell mediated immune response and inflammation of the small intestine. However, not all gluten proteins contain T-cell stimulatory epitopes. Gluten proteins are encoded by multigene loci present on chromosomes 1 and 6 of the three different genomes of hexaploid bread wheat (Triticum aestivum) (AABBDD).     

One-step refolding and purification of disulfide-containing proteins with a C-terminal MESNA thioester

Background  

Expression systems based on self-cleavable intein domains allow the generation of recombinant proteins with a C-terminal thioester. This uniquely reactive C-terminus can be used in native chemical ligation reactions to introduce synthetic groups or to immobilize proteins on surfaces and nanoparticles. Unfortunately, common refolding procedures for recombinant proteins that contain disulfide bonds do not preserve the thioester functionality and therefore novel refolding procedures need to be developed.     

Recombining overlapping BACs into a single larger BAC

Background  

BAC clones containing entire mammalian genes including all the transcribed region and long range controlling elements are very useful for functional analysis. Sequenced BACs are available for most of the human and mouse genomes and in many cases these contain intact genes. However, large genes often span more than one BAC, and single BACs covering the entire region of interest are not available. Here we describe a system for linking two or more overlapping BACs into a single clone by homologous recombination.     

Nucleic acid chaperons: a theory of an RNA-assisted protein folding

Background  

Proteins are assumed to contain all the information necessary for unambiguous folding (Anfinsen's principle). However, ab initio structure prediction is often not successful because the amino acid sequence itself is not sufficient to guide between endless folding possibilities. It seems to be a logical to try to find the "missing" information in nucleic acids, in the redundant codon base.     

Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

Background  

It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood.     

Transfer RNA modifications and genes for modifying enzymes in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Background  

In all domains of life, transfer RNA (tRNA) molecules contain modified nucleosides. Modifications to tRNAs affect their coding capacity and influence codon-anticodon interactions. Nucleoside modification deficiencies have a diverse range of effects, from decreased virulence in bacteria, neural system disease in human, and gene expression and stress response changes in plants. The purpose of this study was to identify genes involved in tRNA modification in the model plant Arabidopsis thaliana, to understand the function of nucleoside modifications in plant growth and development.     

Rule-based spatial modeling with diffusing,geometrically constrained molecules

Background  

We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined.     

The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate

Background  

Secondary metabolism in Serratia sp. ATCC 39006 (Serratia 39006) is controlled via a complex network of regulators, including a LuxIR-type (SmaIR) quorum sensing (QS) system. Here we investigate the molecular mechanism by which phosphate limitation controls biosynthesis of two antibiotic secondary metabolites, prodigiosin and carbapenem, in Serratia 39006.     

Genetic analysis,structural modeling,and direct coupling analysis suggest a mechanism for phosphate signaling in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Background

Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB. The PhoR histidine kinase is responsible for phosphorylating/dephosphorylating the response regulator, PhoB, which controls the expression of genes that aid growth in low phosphate conditions. The mechanism by which PhoR receives a signal of environmental phosphate levels has remained elusive. A transporter complex composed of the PstS, PstC, PstA, and PstB proteins as well as a negative regulator, PhoU, have been implicated in signaling environmental phosphate to PhoR.

Results

This work confirms that PhoU and the PstSCAB complex are necessary for proper signaling of high environmental phosphate. Also, we identify residues important in PhoU/PhoR interaction with genetic analysis. Using protein modeling and docking methods, we show an interaction model that points to a potential mechanism for PhoU mediated signaling to PhoR to modify its activity. This model is tested with direct coupling analysis.

Conclusions

These bioinformatics tools, in combination with genetic and biochemical analysis, help to identify and test a model for phosphate signaling and may be applicable to several other systems.

     

Some properties of the walls of metaxylem vessels of maize roots,including tests of the wettability of their lumenal wall surfaces

Background and Aims

Since the proposal of the cohesion theory there has been a paradox that the lumenal surface of vessels is rich in hydrophobic lignin, while tension in the rising sap requires adhesion to a hydrophilic surface. This study sought to characterize the strength of that adhesion in maize (Zea mays), the wettability of the vessel surface, and to reconcile this with its histochemical and physical nature.

Methods

Wettability was assessed by emptying the maize root vessels of sap, perfusing them with either water or oil, and examining the adhesion (as revealed by contact angles) of the two liquids to vessel walls by cryo-scanning electron microscopy. The phobicity of the lumenal surface was also assessed histochemically with hydrophilic and hydrophobic probes.

Key Results

Pit borders in the lumen-facing vessel wall surface were wetted by both sap/water and oil. The attraction for oil was weaker: water could replace oil but not vice versa. Pit apertures repelled oil and were strongly stained by hydrophilic probes. Pit chambers were probably hydrophilic. Oil never entered the pits. When vessels were emptied and cryo-fixed immediately, pit chambers facing away from the vessels were always sap-filled. Pit chambers facing vessel lumens were either sap- or gas-filled. Sap from adjoining tracheary elements entering empty vessels accumulated on the lumenal surface in hemispherical drops, which spread out with decreasing contact angles to fill the lumen.

Conclusions

The vessel lumenal surface has a dual nature, namely a mosaic of hydrophilic and hydrophobic patches at the micrometre scale, with hydrophilic predominating. A key role is shown, for the first time, of overarching borders of pits in determining the dual nature of the surface. In gas-filled (embolized) vessels they are hydrophobic. When wetted by sap (vessels refilling or full) they are hydrophilic. A hypothesis is proposed to explain the switch between the two states.     

Using hexamers to predict cis-regulatory motifs in Drosophila

Background  

Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered.