Shifted Transversal Design smart-pooling for high coverage interactome mapping

X, Xin; Rual, Jean François; Hirozane-Kishikawa, Tomoko; Hill, David E.; Vidal, Marc; Boone, Charles; Thierry‐Mieg, Nicolas

doi:10.1101/gr.090019.108

Cited by 36 publications

(31 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…TOE-2 is distantly related to vertebrate proteins that contain a GAP domain in addition to their DEP domain (Arur et al, 2009). Although TOE-2 lacks a GAP domain, it can bind to the worm ortholog of GRAF, which contains a RhoGAP domain (Xin et al, 2009(Xin et al, , 2013. It is not known whether this interaction is relevant in the context of the Q.p lineage, but it suggests that TOE-2 might regulate Rho-family GTPases.…”

Section: Toe-2 Localizes Dynamically During the Divisions Of Q And Qpmentioning

confidence: 95%

The DEP domain-containing protein TOE-2 promotes apoptosis in the Q lineage of C. elegans through two distinct mechanisms

2014

View full text Add to dashboard Cite

Neuroblast divisions in the nematode Caenorhabditis elegans often give rise to a larger neuron and a smaller cell that dies. We have previously identified genes that, when mutated, result in neuroblast divisions that generate daughter cells that are more equivalent in size. This effect correlates with the survival of daughter cells that would normally die. We now describe a role for the DEP domain-containing protein TOE-2 in promoting the apoptotic fate in the Q lineage. TOE-2 localized at the plasma membrane and accumulated in the cleavage furrow of the Q.a and Q.p neuroblasts, suggesting that TOE-2 might position the cleavage furrow asymmetrically to generate daughter cells of different sizes. This appears to be the case for Q.a divisions where loss of TOE-2 led to a more symmetric division and to survival of the smaller Q.a daughter. Localization of TOE-2 to the membrane is required for this asymmetry, but, surprisingly, the DEP domain is dispensable. By contrast, loss of TOE-2 led to loss of the apoptotic fate in the smaller Q.p daughter but did not affect the size asymmetry of the Q.p daughters. This function of TOE-2 required the DEP domain but not localization to the membrane. We propose that TOE-2 ensures an apoptotic fate for the small Q.a daughter by promoting asymmetry in the daughter cell sizes of the Q.a neuroblast division but by a mechanism that is independent of cell size in the Q.p division.

show abstract

Section: Toe-2 Localizes Dynamically During the Divisions Of Q And Qpmentioning

confidence: 95%

The DEP domain-containing protein TOE-2 promotes apoptosis in the Q lineage of C. elegans through two distinct mechanisms

2014

View full text Add to dashboard Cite

show abstract

“…The pools are then characterized by INSeq, and the presence/absence pattern of a given insertion site across the pools reflects the unique pattern associated with the corresponding bacterial strain in the multi-well collection. Alternative pooling patterns that use larger numbers of pools to further reduce the likelihood of mistaking one strain for another can also be considered 3–5 . These alternatives would be appropriate if many mutants in the population were likely to carry insertions at the same location in the genome, but require greater effort in preparing libraries because of the increased number of pools.…”

Section: Introductionmentioning

confidence: 99%

Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries

Goodman

Wu²,

Gordon³

2011

Nat Protoc

159

183

View full text Add to dashboard Cite

Insertion Sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial species. INSeq is based on a modified mariner transposon containing MmeI sites at its ends, allowing cleavage at chromosomal sites 16–17bp from the inserted transposon. Genomic regions adjacent to the transposons are amplified by linear PCR with a biotinylated primer. Products are bound to magnetic beads, digested with MmeI, and barcoded with sample-specific linkers appended to each restriction fragment. After limited PCR amplification, fragments are sequenced using a high-throughput instrument. The sequence of each read can be used to map the location of a transposon in the genome. Read count measures the relative abundance of that mutant in the population. Solid-phase library preparation makes this protocol rapid (18h), easy to scale-up, amenable to automation, and useful for a variety of samples. A protocol for characterizing libraries of transposon mutant strains clonally arrayed in multi-well format is provided.

show abstract

“…Combinatorial group testing 1 has found applications in drug and DNA library screening (the literature is large, see [40,28,50,27] and references thereof), multiple access control protocols [5,49], live baiting of DoS attackers [29], data forensics [24] and data streams [13], among others. The reader is referred to the standard monograph on group testing for more details [16].…”

Section: Introductionmentioning

confidence: 99%

Recovering simple signals

Gilbert

Hemenway

Rudra

et al. 2012

2012 Information Theory and Applications Workshop

View full text Add to dashboard Cite

Abstract. The primary goal of compressed sensing and (non-adaptive) combinatorial group testing is to recover a sparse vector x from an underdetermined set of linear equations Φx = y. Both problems entail solving Φx = y given Φ and y but they use different models of arithmetic, different models of randomness models for Φ, and different guarantees upon the solution x and the class of signals from which it is drawn. In [32], Lipton introduced a model for error correction where the channel is computationally bounded, subject to standard cryptographic assumptions, and produces the error vector x that must be found and then corrected. This has been extended in [24, 34] to create more efficient schemes against polynomial and logspace bounded channels. Inspired by these results in error correction, we view compressed sensing and combinatorial group testing as an adversarial process, where Mallory the adversary produces the vector x to be measured, with limited information about the matrix Φ. We define a number of computationally bounded models for Mallory and show that there are significant gains (in the minimum number of measurements) to be had by relaxing the model from adversarial to computationally or information-theoretically bounded, and not too much (in some cases, nothing at all) is lost by assuming these models over oblivious or statistical models. We also show that differences in adversarial power give rise to different lower bounds for the number of measurements required to defeat such an adversary. By contrast we show that randomized one pass log space streaming Mallory is almost as powerful as a fully adversarial one for group testing while for compressed sensing such an adversary as weak as an oblivious one.

show abstract

Shifted Transversal Design smart-pooling for high coverage interactome mapping

Cited by 36 publications

References 24 publications

The DEP domain-containing protein TOE-2 promotes apoptosis in the Q lineage of C. elegans through two distinct mechanisms

The DEP domain-containing protein TOE-2 promotes apoptosis in the Q lineage of C. elegans through two distinct mechanisms

Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries

Recovering simple signals

Contact Info

Product

Resources

About