Identification of PLX4032‐resistance mechanisms and implications for novel RAF inhibitors

BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole‐exome sequencing of drug‐resistant BRAF^V600K melanoma cells. We further describe a new screening approach, a genome‐wide piggyBac mutagenesis screen that revealed clinically relevant aberrations (N‐terminal BRAF truncations and CRAF overexpression). The novel BRAF mutation, a Leu505 to His substitution (BRAF^L505H), is the first resistance‐conferring second‐site mutation identified in BRAF mutant cells. The mutation replaces a small nonpolar amino acid at the BRAF‐PLX4032 interface with a larger polar residue. Moreover, we show that BRAF^L505H, found in human prostate cancer, is itself a MAPK‐activating, PLX4032‐resistant oncogenic mutation. Lastly, we demonstrate that the PLX4032‐resistant melanoma cells are sensitive to novel, next‐generation BRAF inhibitors, especially the ‘paradox‐blocker’ PLX8394, supporting its use in clinical trials for treatment of melanoma patients with BRAF‐mutations.     

A decision support tool for the management of freshwater pest fish incursions in Australia

There are no national emergency response arrangements for freshwater pest fish incursions in Australia. Individual States and Territories vary widely in their current response arrangements to freshwater pest fish incursions, with many being dealt with on an ad‐hoc basis and with varying degrees of efficacy. In recognition of this, the Invasive Animals Cooperative Research Centre funded a project to ‘Advance the development of national emergency response arrangements for freshwater fish incursions in Australia’. One of the recommendations of this project was creating a web‐based support tool (DST) to provide direction and assistance in managing freshwater pest fish incursions. This article describes the DST created. The DST leads the user through a series of questions relating to the species sighting, details of the fish and its capture, and site information at a particular location. These questions address issues that managers must consider when choosing appropriate control techniques. Information entered in two sections (site details and fish details) influence the suggested control techniques. The final product of the DST is a standard online report that contains a summary of all information entered and a ranking of the most common control techniques used in Australia. The report is then submitted to and assessed by the relevant State Government authority responsible for the management of freshwater pest fish incursions. Managers are then able to consider their options, taking into consideration current permits, resources and capability. The DST is anticipated to maximize the speed and quality of freshwater pest fish incursion reporting and to help the responsible government agency decide on the most appropriate management action. The DST will also provide government agency staff access to other relevant information and facilitate consistency in the decision‐making approach by government agencies throughout Australia.     

Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage

The similarity of two nucleotide sequences is often expressed in terms of evolutionary distance, a measure of the amount of change needed to transform one sequence into the other. Given two sequences with a small distance between them, can their similarity be explained by their base composition alone? The nucleotide order of these sequences contributes to their similarity if the distance is much smaller than their average permutation distance, which is obtained by calculating the distances for many random permutations of these sequences. To determine whether their similarity can be explained by their dinucleotide and codon usage, random sequences must be chosen from the set of permuted sequences that preserve dinucleotide and codon usage. The problem of choosing random dinucleotide and codon-preserving permutations can be expressed in the language of graph theory as the problem of generating random Eulerian walks on a directed multigraph. An efficient algorithm for generating such walks is described. This algorithm can be used to choose random sequence permutations that preserve (1) dinucleotide usage, (2) dinucleotide and trinucleotide usage, or (3) dinucleotide and codon usage. For example, the similarity of two 60-nucleotide DNA segments from the human beta-1 interferon gene (nucleotides 196-255 and 499-558) is not just the result of their nonrandom dinucleotide and codon usage.      

Metabolism of mono-and dichlorinated guaiacols by Rhodococcus ruber CA16

The metabolism of chloroguaiacols by a soil bacterium was studied. The strain was isolated by enrichment with guaiacol as the sole carbon and energy source, and identified as a Rhodococcus ruber CA16. None of seven chlorinated, guaiacols supported bacterial growth. However, ultraviolet spectroscopy chloride release, and oxygen consumption showed that resting cells grown on guaiacol degraded completely 4-chloroguaiacol 5-chloroguaiacol and 6-chloroguaiacol and, to a lesser extent, 4,5-dichloroguaiacol Gas chromatographic analysis suggested microbial formation of 4-chlorocatechol and 4,5-dichlorocatechol from 4-chloroguaiacol and 4,5-dichloroguaiacol, respectively. Although mono-and dichloroguaiacols did not affect the strain's ability to grow on guaiacol, chlorocatechols completely arrested growth. The role of chlorocatechols in chloroguaiacol metabolism by this guaiacol-degrading bacterial strain is discussed.     

The genes that encode the gonococcal transferrin binding proteins,TbpB and TbpA,are differentially regulated by MisR under iron‐replete and iron‐depleted conditions

Neisseria gonorrhoeae produces two transferrin binding proteins, TbpA and TbpB, which together enable efficient iron transport from human transferrin. We demonstrate that expression of the tbp genes is controlled by MisR, a response regulator in the two‐component regulatory system that also includes the sensor kinase MisS. The tbp genes were up‐regulated in the misR mutant under iron‐replete conditions but were conversely down‐regulated in the misR mutant under iron‐depleted conditions. The misR mutant was capable of transferrin‐iron uptake at only 50% of wild‐type levels, consistent with decreased tbp expression. We demonstrate that phosphorylated MisR specifically binds to the tbpBA promoter and that MisR interacts with five regions upstream of the tbpB start codon. These analyses confirm that MisR directly regulates tbpBA expression. The MisR binding sites in the gonococcus are only partially conserved in Neisseria meningitidis, which may explain why tbpBA was not MisR‐regulated in previous studies using this related pathogen. This is the first report of a trans‐acting protein factor other than Fur that can directly contribute to gonococcal tbpBA regulation.     

mlo‐based powdery mildew resistance in hexaploid bread wheat generated by a non‐transgenic TILLING approach

Wheat is one of the most widely grown cereal crops in the world and is an important food grain source for humans. However, wheat yields can be reduced by many abiotic and biotic stress factors, including powdery mildew disease caused by Blumeria graminis f.sp. tritici (Bgt). Generating resistant varieties is thus a major effort in plant breeding. Here, we took advantage of the non‐transgenic Targeting Induced Lesions IN Genomes (TILLING) technology to select partial loss‐of‐function alleles of TaMlo, the orthologue of the barley Mlo (Mildew resistance locus o) gene. Natural and induced loss‐of‐function alleles (mlo) of barley Mlo are known to confer durable broad‐spectrum powdery mildew resistance, typically at the expense of pleiotropic phenotypes such as premature leaf senescence. We identified 16 missense mutations in the three wheat TaMlo homoeologues, TaMlo‐A1, TaMlo‐B1 and TaMlo‐D1 that each lead to single amino acid exchanges. Using transient gene expression assays in barley single cells, we functionally analysed the different missense mutants and identified the most promising candidates affecting powdery mildew susceptibility. By stacking of selected mutant alleles we generated four independent lines with non‐conservative mutations in each of the three TaMlo homoeologues. Homozygous triple mutant lines and surprisingly also some of the homozygous double mutant lines showed enhanced, yet incomplete, Bgt resistance without the occurrence of discernible pleiotropic phenotypes. These lines thus represent an important step towards the production of commercial non‐transgenic, powdery mildew‐resistant bread wheat varieties.