Methods are given for a screen using whole-genome multiplex sequencing in the filamentous fungus Aspergillus nidulans. Novel alleles of the molecular motor cytoplasmic dynein identified in this screen reveal that different dynein cargoes have distinct requirements for motor performance.

Abstract:Weakly Interacting Massive Particles (WIMPs) may constitute a large fraction of the matter in the Universe. There are excess events in the data of DAMA/LIBRA, CoGeNT, CRESST-II, and recently CDMS-Si, which could be consistent with WIMP masses of approximately 10 GeV/c 2 . However, for M DM > 10 GeV/c 2 null results of the CDMS-Ge, XENON, and LUX detectors may be in tension with the potential detections for certain dark matter scenarios and assuming a certain light response.We propose the use of a new class of biological dark matter (DM) detectors to further examine this light dark matter hypothesis, taking advantage of new signatures with low atomic number targets, Two types of biological DM detectors are discussed here: DNA-based detectors and enzymatic reactions (ER) based detectors. In the case of DNA-based detectors, we discuss a new implementation. In the case of ER detectors, there are four crucial phases of the detection process: a) change of state due to energy deposited by a particle; b) amplification due to the release of energy derived from the action of an enzyme on its substrate; c) sustainable but non-explosive enzymatic reaction; d) self-termination due to the denaturation of the enzyme, when the temperature is raised. This paper provides information of how to design as well as optimize these four processes. 1) INTRODUCTION In the mid 20th century, new classes of particle/radiation detectors were introduced about every 5 years. The last new classes of detectors were introduced about 30 and 25 years ago, namely cryogenic particle detectors and liquid noble gas detectors, respectively. Yet there are needs of physics and biology which require new classes of detectors with nano-metric spatial resolution e.g. detection of Dark Matter (DM) candidates and detectors for massspectroscopy.The first generation of particle/radiation detectors consisted of photographic emulsions and gas detectors. The majority of modern particle detectors are liquids and solid-state detectors. All of these detectors have, as output, either photons or electrons, which are easy to count with modern photonics and/or electronics.We propose a new class of detectors, which use thermal processes or molecular transformations to detect particle interaction effect(s). One of the byproducts of the development of molecular biology and nanotechnology is that we now understand and can engineer material properties at a scale of a few nanometers. This includes better understanding of heat propagation processes at the nanoscale. We can produce a wide variety of nano-size objects and order them spatially. It becomes possible to manipulate the flow of heat just as we manipulate the flow of 1 electrons in solid-state devices. In a sense, the development of Superheated Superconducting Colloid [26] and other cryogenic bolometers [18,19,24] were a first step in this direction. However, they operate at cryogenic temperatures, which facilitate thermal engineering but make their implementation and operation more difficult. In this paper, we pr...

4-Nitroquinoline 1-oxide (4-NQO) is a highly carcinogenic chemical that induces mutations in bacteria, fungi, and animals through the formation of bulky purine adducts. 4-NQO has been used as a mutagen for genetic screens and in both the study of DNA damage and DNA repair. In the model eukaryote Aspergillus nidulans, 4-NQO−based genetic screens have been used to study diverse processes, including gene regulation, mitosis, metabolism, organelle transport, and septation. Early work during the 1970s using bacterial and yeast mutation tester strains concluded that 4-NQO was a guanine-specific mutagen. However, these strains were limited in their ability to determine full mutagenic potential, as they could not identify mutations at multiple sites, unlinked suppressor mutations, or G:C to C:G transversions. We have now used a whole genome resequencing approach with mutant strains generated from two independent genetic screens to determine the full mutagenic spectrum of 4-NQO in A. nidulans. Analysis of 3994 mutations from 38 mutant strains reveals that 4-NQO induces substitutions in both guanine and adenine residues, although with a 19-fold preference for guanine. We found no association between mutation load and mutagen dose and observed no sequence bias in the residues flanking the mutated purine base. The mutations were distributed randomly throughout most of the genome. Our data provide new evidence that 4-NQO can potentially target all base pairs. Furthermore, we predict that current practices for 4-NQO−induced mutagenesis are sufficient to reach gene saturation for genetic screens with feasible identification of causative mutations via whole genome resequencing.

Motivation Over the last few years, the field of protein structure prediction has been transformed by increasingly-accurate contact prediction software. These methods are based on the detection of coevolutionary relationships between residues from multiple sequence alignments. However, despite speculation, there is little evidence of a link between contact prediction and the physico-chemical interactions which drive amino-acid coevolution. Furthermore, existing protocols predict only a fraction of all protein contacts and it is not clear why some contacts are favoured over others. Using a dataset of 863 protein domains, we assessed the physico-chemical interactions of contacts predicted by CCMpred, MetaPSICOV, and DNCON2, as examples of direct coupling analysis, meta-prediction, and deep learning. Results We considered correctly-predicted contacts and compared their properties against the protein contacts that were not predicted. Predicted contacts tend to form more bonds than non-predicted contacts, which suggests these contacts may be more important than contacts that were not predicted. Comparing the contacts predicted by each method, we found that metaPSICOV and DNCON2 favour accuracy whereas CCMPred detects contacts with more bonds. This suggests that the push for higher accuracy may lead to a loss of physico-chemically important contacts. These results underscore the connection between protein physico-chemistry and the coevolutionary couplings that can be derived from multiple sequence alignments. This relationship is likely to be relevant to protein structure prediction and functional analysis of protein structure and may be key to understanding their utility for different problems in structural biology. Availability We use publicly-available databases. Our code is available for download at http://opig.stats.ox.ac.uk/. Supplementary information Supplementary information is available at Bioinformatics online.