Highly efficient CRISPR-mediated gene editing in a rotifer.

Rotifers have been studied in the laboratory and field for over 100 years in investigations of microevolution, ecological dynamics, and ecotoxicology. In recent years, rotifers have emerged as a model system for modern studies of the molecular mechanisms of genome evolution, development, DNA repair, aging, life history strategy, and desiccation tolerance. However, a lack of gene editing tools and transgenic strains has limited the ability to link genotype to phenotype and dissect molecular mechanisms. To facilitate genetic manipulation and the creation of reporter lines in rotifers, we developed a protocol for highly efficient, transgenerational, CRISPR-mediated gene editing in the monogonont rotifer Brachionus manjavacas by microinjection of Cas9 protein and synthetic single-guide RNA into the vitellaria of young amictic (asexual) females. To demonstrate the efficacy of the method, we created knockout mutants of the developmental gene vasa and the DNA mismatch repair gene mlh3. More than half of mothers survived injection and produced offspring. Genotyping these offspring and successive generations revealed that most carried at least 1 CRISPR-induced mutation, with many apparently mutated at both alleles. In addition, we achieved precise CRISPR-mediated knock-in of a stop codon cassette in the mlh3 locus, with half of injected mothers producing F2 offspring with an insertion of the cassette. Thus, this protocol produces knockout and knock-in CRISPR/Cas9 editing with high efficiency, to further advance rotifers as a model system for biological discovery.

Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution.

Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single observation, single-cell sequencing isolates and amplifies genetic material from individual cells, thereby preserving the information about the origin of the sequences. However, single-cell data are more error-prone than bulk sequencing data due to the limited genomic material available per cell. Here, we present error and mutation models for evolutionary inference of single-cell data within a mature and extensible Bayesian framework, BEAST2. Our framework enables integration with biologically informative models such as relaxed molecular clocks and population dynamic models. Our simulations show that modeling errors increase the accuracy of relative divergence times and substitution parameters. We reconstruct the phylogenetic history of a colorectal cancer patient and a healthy patient from single-cell DNA sequencing data. We find that the estimated times of terminal splitting events are shifted forward in time compared to models which ignore errors. We observed that not accounting for errors can overestimate the phylogenetic diversity in single-cell DNA sequencing data. We estimate that 30-50% of the apparent diversity can be attributed to error. Our work enables a full Bayesian approach capable of accounting for errors in the data within the integrative Bayesian software framework BEAST2.

Resources and Attitudes Influence Acculturation of Deaf Children with Cochlear Implants.

Early detection of hearing loss leads to early intervention-related decisions. Most children with cochlear implants (CIs) are born to hearing parents. Prior evidence suggests that this increased access to oral communication and the "hearing" world means oral communication is prioritized by hearing parents. Language plays a key role within culture and these communication decisions are likely to be associated with children's level of d/Deaf acculturation. This study was based on qualitative interviews. Thirty-two people associated with 14 children were interviewed; these were parents of children with CIs, four children over age 11 years, and teachers of 13 of the children. The study aimed to investigate parental communication decisions on child/family d/Deaf acculturation and the role of access to resources on children's d/Deaf acculturation development. Findings indicate two profiles of family acculturation-oral and bicultural and point to a possible relationship between access to resources and parents' decision-making process.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales.

Evolutionary models account for either population- or species-level processes but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.[Caninae; fossilized birth-death; molecular clock; multispecies coalescent; phylogenetics; species trees.].

Pyridine interaction with γ-CuI: synergy between molecular dynamics and molecular orbital approaches to molecule/surface interactions.

We have used a synergistic computational approach merging Molecular Dynamics (MD) simulations with density functional theory (DFT) to investigate the mechanistic aspects of chemisorption of pyridine (Py) molecules on copper iodide. The presence of both positive and negative ions at the metal halide surface presents a chemical environment in which pyridine molecules may act as charge donors and/or acceptors. Computational results reveal that Py molecules interact with the γ-CuI(111) surface owing to a combination of noncovalent Cu⋯N, Cu/I⋯π/π*, and hydrogen bonding interactions as determined via Natural Bonding Orbitals (NBO). Introduction of surface defect sites alters the interaction dynamics, resulting in a "localizing effect" in which the Py molecules clump together within the defect site. Significant enhancement of hydrogen bonding between C-H σ* and I 6p orbitals results in more tightly surface-bound Py molecules. Our findings provide a platform for understanding the interaction between Py and Py-derivative vapors and metal-based surfaces that contain both electron acceptor and donor atoms.

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand.

Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders. These outbreaks originated at the border via isolating returnees, airline workers, and cargo vessels. Because a public health system was informed by real-time viral genomic sequencing and complete genomes typically were available within 12 hours of community-based positive COVID-19 test results, every outbreak was well-contained. A total of 225 community cases resulted in 3 deaths. Real-time genomics were essential for establishing links between cases when epidemiologic data could not do so and for identifying when concurrent outbreaks had different origins.

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand.

Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.

Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing.

Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.

Estimating Epidemic Incidence and Prevalence from Genomic Data.

Modern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death, or behavior change). Birth-death and coalescent processes have been introduced to model the stochastic dynamics of epidemic spread under common epidemiological models such as the SIS and SIR models and are successfully used to infer phylogenetic trees together with transmission (birth) and removal (death) rates. These methods either integrate analytically over past incidence and prevalence to infer rate parameters, and thus cannot explicitly infer past incidence or prevalence, or allow such inference only in the coalescent limit of large population size. Here, we introduce a particle filtering framework to explicitly infer prevalence and incidence trajectories along with phylogenies and epidemiological model parameters from genomic sequences and case count data in a manner consistent with the underlying birth-death model. After demonstrating the accuracy of this method on simulated data, we use it to assess the prevalence through time of the early 2014 Ebola outbreak in Sierra Leone.

The Epidemiology of Noise Sensitivity in New Zealand.

BACKGROUND: Sensitivity to noise, or nuisance sounds that interrupt relaxation and task-related activities, has been shown to vary significantly across individuals. The current study sought to uncover predictors of noise sensitivity, focussing on possible social and cultural determinants, including social position, education, ethnicity, gender, and the presence of an illness. METHOD: Data were collected from 746 New Zealand adults residing in 6 areas differentiated by social position. Participants responded to questions probing personal characteristics, noise sensitivity, illness, neighbourhood problems, and noise annoyance. It was hypothesized that those in high-deprivation areas and/or experiencing illness report higher levels of noise sensitivity. RESULTS: Approximately 50 and 10% of the participants reported being moderately or very noise sensitive, respectively. Significant predictors of noise sensitivity included age, length of residence, level of social deprivation, and self-reported illness. CONCLUSION: There is evidence of social determinants of noise sensitivity, including social position and residential factors.

Understanding the vapochromic response of mixed copper(i) iodide/silver(i) Iodide nanoparticles toward dimethyl sulfide.

We report on the vapochromic behavior of a series of homo- and heterometallic copper(i) iodide/silver(i) iodide nanoparticles when exposed to dimethyl sulfide (DMS) vapor. These systems show remarkable colorimetric sensing behavior via emission color upon DMS exposure, shifting from pink to green emission. Kinetics measurements of CuI/AgI nanoparticle reactions with DMS show a significant rate increase with increasing Ag(i) content. However, luminescence spectroscopy and X-ray diffraction of the post-exposure samples with varying Ag(i) content reveal that the luminophore is identical in all cases and contains no Ag(i) ions. To rationalize the experimental observations and determine the vapochromic response mechanism, molecular dynamic calculations were performed on model (111) cation-terminated surfaces of copper iodide crystals doped with variable amounts of silver. Computational studies indicate that heterometallic Cu/Ag systems have a stronger binding affinity towards DMS vapor molecules than homometallic CuI and that embedding of the DMS molecules into the surface is the primary intermediate by which the vapochromic response occurs.

Linking environmental factors with reflex action mortality predictors, physiological stress, and post-release movement behaviour to evaluate the response of white sturgeon (Acipenser transmontanus Richardson, 1836) to catch-and-release angling.

White sturgeon are the largest freshwater fish in North America and are the focus of an intense catch-and-release (C&R) fishery; the effects are largely unknown. We assessed the effect of fight and handling time, water temperature, river discharge rate, and fish size on physiological and reflex impairment responses of wild white sturgeon to angling. Sixty of these fish were tagged with acoustic transmitters to assess survival and post-release behaviour. Survival was high (100%). Water temperature and discharge influenced post-capture blood physiology. Specifically, lactate, chloride, and cortisol concentrations were elevated in individuals fought longer, and captured at higher water temperatures and river discharge. Cortisol was affected by fish size, with lower concentrations found in larger individuals. Only lactate and chloride were positively related to reflex impairment scores. Post-release movements were correlated with physiological state, fight characteristics and the environment. Specifically, higher blood lactate and chloride and those with longer fight times moved shorter distances after release. Contrastingly, higher levels of circulating glucose and potassium, as well as larger fish captured during periods of high discharge moved longer distances. Sturgeon tended to move shorter distances and at slower rates when reflex impairment was high, although reflex impairment in general did not explain a significant proportion of the variance in any movement metric. Our results show intriguing variance in the physiological and behavioural response of individual white sturgeon to C&R angling, with some degree of environmental dependence, and highlights the importance of understanding drivers of such variation when managing fisheries.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.

Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers.

BACKGROUND: Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2-4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair. RESULTS: We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75-100% of genes involved in MMR and HR are present in 0-2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3-8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes. CONCLUSION: The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids.

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.

The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth­death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ∼12.7 ∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed.

Health-related quality of life is impacted by proximity to an airport in noise-sensitive people.

INTRODUCTION: The aim of the study was to determine whether those who are noise sensitive are more adversely affected by airport noise than those who are not noise sensitive. PARTICIPANTS AND METHODS: One area was very close to Wellington International Airport and the other was distant from the airport and any other major sources of noise such as motorways and railways. Noise sensitivity was self-rated on a three-point scale as follows: non-noise sensitive, moderately noise sensitive, or highly noise sensitive. Statistical analysis consisted of analyses of variance using the domains of the WHOQOL score with the year, area (airport or the control), and noise sensitivity as covariates. RESULTS: Noise-sensitive people were found to have a significantly poorer HRQOL than others when they lived near an airport, but not when they lived in the control area. The same effect was present at both of the time points investigated, suggesting that it is a general finding. DISCUSSION: This finding is consistent with similar studies using the WHOQOL-BREF for investigating noise from road traffic, suggesting consistency in effect across transport noise sources.

Thiamine Levels in Muscle and Eggs of Adult Pacific Salmon from the Fraser River, British Columbia.

Multiple species and stocks of Pacific salmon Oncorhynchus spp. have experienced large declines in the number of returning adults over a wide region of the Pacific Northwest due to poor marine survival (low smolt-to-adult survival rates). One possible explanation for reduced survival is thiamine deficiency. Thiamine (vitamin B1 ) is an essential vitamin with an integral role in many metabolic processes, and thiamine deficiency is an important cause of salmonid mortality in the Baltic Sea and in the Laurentian Great Lakes. To assess this possibility, we (1) compared muscle thiamine content over time in a holding experiment using Fraser River (British Columbia) Sockeye Salmon O. nerka to establish whether adults that died during the holding period had lower thiamine levels than survivors, (2) measured infectious loads of multiple pathogens in held fish, and (3) measured egg thiamine content from four species of Pacific salmon collected on Fraser River spawning grounds. Chinook Salmon O. tshawytscha had the lowest egg thiamine, followed by Sockeye Salmon; however, egg thiamine concentrations were above levels known to cause overt fry mortality. Thiamine vitamers in the muscle of Fraser River adult Sockeye Salmon shifted over a 13-d holding period, with a precipitous decline in thiamine pyrophosphate (the active form of thiamine used in enzyme reactions) in surviving fish. Survivors also carried lower loads of Flavobacterium psychrophilum than fish that died during in the holding period. Although there is no evidence of thiamine deficiency in the adults studied, questions remain about possible thiamine metabolism-fish pathogen relationships that influence survival.

Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system.

BACKGROUND: Understanding gene expression changes over lifespan in diverse animal species will lead to insights to conserved processes in the biology of aging and allow development of interventions to improve health. Rotifers are small aquatic invertebrates that have been used in aging studies for nearly 100 years and are now re-emerging as a modern model system. To provide a baseline to evaluate genetic responses to interventions that change health throughout lifespan and a framework for new hypotheses about the molecular genetic mechanisms of aging, we examined the transcriptome of an asexual female lineage of the rotifer Brachionus manjavacas at five life stages: eggs, neonates, and early-, late-, and post-reproductive adults. RESULTS: There are widespread shifts in gene expression over the lifespan of B. manjavacas; the largest change occurs between neonates and early reproductive adults and is characterized by down-regulation of developmental genes and up-regulation of genes involved in reproduction. The expression profile of post-reproductive adults was distinct from that of other life stages. While few genes were significantly differentially expressed in the late- to post-reproductive transition, gene set enrichment analysis revealed multiple down-regulated pathways in metabolism, maintenance and repair, and proteostasis, united by genes involved in mitochondrial function and oxidative phosphorylation. CONCLUSIONS: This study provides the first examination of changes in gene expression over lifespan in rotifers. We detected differential expression of many genes with human orthologs that are absent in Drosophila and C. elegans, highlighting the potential of the rotifer model in aging studies. Our findings suggest that small but coordinated changes in expression of many genes in pathways that integrate diverse functions drive the aging process. The observation of simultaneous declines in expression of genes in multiple pathways may have consequences for health and longevity not detected by single- or multi-gene knockdown in otherwise healthy animals. Investigation of subtle but genome-wide change in these pathways during aging is an important area for future study.

Automated microbeam observation environment for biological analysis-Custom portable environmental control applied to a vertical microbeam system.

Vertical Microbeams (VMB) are used to irradiate individual cells with low MeV energy ions. The irradiation of cells using VMBs requires cells to be removed from an incubator; this can cause physiological changes to cells because of the lower CO2 concentration, temperature and relative humidity outside of the incubator. Consequently, for experiments where cells require irradiation and observation for extended time periods, it is important to provide a controlled environment. The highly customised nature of the microscopes used on VMB systems means that there are no commercially available environmentally controlled microscope systems for VMB systems. The Automated Microbeam Observation Environment for Biological Analysis (AMOEBA) is a highly flexible modular environmental control system used to create incubator conditions on the end of a VMB. The AMOEBA takes advantage of the recent "maker" movement to create an open source control system that can be easily configured by the user to fit their control needs even beyond VMB applications. When applied to the task of controlling cell medium temperature, CO2 concentration and relative humidity on VMBs it creates a stable environment that allows cells to multiply on the end of a VMB over a period of 36 h, providing a low-cost (costing less than $2700 to build), customisable alternative to commercial time-lapse microscopy systems. AMOEBA adds the potential of VMBs to explore the long-term effects of radiation on single cells opening up new research areas for VMBs.

An ecological approach to hearing-health promotion in workplaces.

OBJECTIVE: To develop and assess use, acceptability and feasibility of an ecological hearing conservation programme for workplaces. DESIGN: A school-based public health hearing preservation education programme (Dangerous Decibels®) was adapted for workplaces using the Multi-level Approach to Community Health (MATCH) Model. The programme was delivered in small manufacturing companies and evaluated using a questionnaire before the training and at one week and two-months after training. STUDY SAMPLE: Workers (n = 56) from five small manufacturing companies were recruited. RESULTS: There was a significant improvement in knowledge, attitudes and behaviour of workers at the intrapersonal level; in behaviour motivation and safety culture at the interpersonal and organisational levels; and an overall improvement in hearing-health behaviour after two months post-intervention. CONCLUSIONS: The developed programme offers a simple, interactive and theory-based intervention that is well accepted and effective in promoting positive hearing-health behaviour in workplaces.