Open Source Solutions in Experimental Design: An Introduction to the Symposium

The Open Science movement has increased dramatically in popularity with deserved calls to action around transparency, access to resources, and inclusion in our field. However, its practical applications within experimental design have been slow to uptake, with researchers unsure where to even start with the dizzying array of open source hardware and software solutions available. The perceived time investment and unknown cost, especially in implementing open source hardware, has stagnated the implementation of inexpensive experimental solutions, but we sought to increase awareness to lower the barrier to participation in this space. While there are countless technical and financial advantages to integrating open source solutions into every biologist\u27s experimental design, we put an emphasis on the “people” part of the equation in our symposium. This symposium championed innovative experimental designs by early career SICB researchers across all fields of biology, from plants to animals, in the lab or in the field, or even virtually engaging with the public and students. The open science movement operates within community norms that champion transparency, continuous development, and collaboration. These values are congruent with the priorities of reducing barriers to participation in science, and we hope our symposium\u27s collection of open source solutions encourages readers to adopt these or other innovative designs into their own experimentation

Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Abstract Background Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing. Results A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3–4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes. Conclusions M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Open-source Camera Trap for Organism Presence and Underwater Surveillance (OCTOPUS)

This Open-source Camera Trap for Organism Presence and Underwater Surveillance (OCTOPUS) was designed to operate as a motion activated camera trap, deployable at depths of up to 800 ft for ∼72 h deployments. The core components of the OCTOPUS are built off a Raspberry Pi 3B+ with a custom PCB hat which operates a strobe lighting system and a high definition Arducam camera. When an appropriate threshold of motion is detected, the OCTOPUS captures a high-definition image of the subject. Field trials for this system demonstrated its use for cryptic benthic organisms, specifically small octopus (Octopus rubescens). The OCTOPUS collected data on several species allowing the observation and quantification of interspecific and conspecific interactions. This system unlocks the potential of autonomous underwater data collection for a wide range of applications, from species specific observations to large scale ecological assessments