The mathematics of thermal sub-optimality: Nonlinear regression characterization of thermal performance of reptile metabolic rates

Although several approaches have been suggested, there is no broadly accepted single approach for quantitative characterization of thermal performance in ectotherms. I sought to identify the most appropriate non-linear function with which to represent thermal performance of ectothermic metabolic rate, and to interrogate the biological relevance of the thermal parameters of this function. I used published data for exercise-induced metabolic rates of eight species of reptile from a broad phylogenetic base and global distribution. Using an Akaike Information Criterion, I compared 12 different models proposed to characterize thermal performance adapted from a broad range of disciplines, finding that a beta-distribution model described the reptile metabolic rate data most parsimoniously. Using the beta-distribution model, unique functions were parameterized for each species. Four parameters were extracted from each species-specific fit: the temperature coincident with the peak of the thermal performance curve, T opt ; the point at which the function intersected the x-axis, CT max ; and two points indicative of thermal breadth, T d(lower) and T d(upper) . There was a positive relationship between the species’ preferred body temperatures (T pref ) reported in the scientific literature and both T opt and T d(lower) extracted from the species-specific beta functions. While T d(lower) estimates were not different to published T pref values, T opt estimates were statistically higher than T pref . This is consistent with previous observations that the point of peak performance does not match T pref . The predicted CT max also correlated well with published values. The model in its current form was not able to estimate CT min , and this parameter was not explored here, but should be in future research. By providing a quantitative description of the thermal performance, the beta-distribution function offers a new theoretical basis for thermal optimality. I contend that T pref aligns with the mathematical threshold T d(lower) , where metabolic rate is at its maximum prior to thermal inhibition

Understanding the interplay of temperature and moisture on the germination niche to improve management of threatened species impacted by mining

The return of vegetation to mined lands often requires broadcast seeding of diverse native seed mixes. However, seeds are highly adapted to germination windows with specific hydrothermal thresholds that maximize the likelihood of seedling survival, and post-mining landscapes typically offer markedly different hydrothermal conditions than pre-disturbance ecosystems. According to niche theory, generalist species should exhibit broader hydrothermal performance niches than specialist taxa, which may influence the success of recruitment from seeds in post-mining ecological restoration. To test this assumption, the impact of hydrothermal stress (incubation temperature (10–30°C) and osmotic potential (−0.8 to 0 MPa)) on the time to 50% germination (t50) and maximum germination (Gmax) was compared between two narrow-range species of conservation concern (Acacia woodmaniorum and A. karina) restricted to mining-impacted Banded Ironstone Formations (BIF) and three broadly distributed congenerics (A. assimilis, A. exocarpoides, and A. ramulosa). The hydrothermal germination niches of the study species were broadly congruent with hydrothermal conditions of their habitats. The two range-restricted taxa were more tolerant of hydrothermal stress compared to the three widely distributed taxa, suggesting that tolerance of greater hydrothermal stress by both range-restricted Acacia species is likely to be adaptive to establishment in uncontested niche space. Complex interactions between thermal and water stress suggest these environmental gradients may shape the germination niche as well as patterns of plant diversity in BIF ecosystems. This study highlights the importance of quantifying interactions between niche dimensions and their implications for species performance, which will aid future restoration efforts for micro-endemic species impacted by mining

Malaria Data by District: An open-source web application for increasing access to malaria information

In recent years, the mapping of diseases has improved considerably in extent, resolution and accuracy (Kraemer et al., 2016). Increasingly, data and related spatial outputs are being made publicly available (Briand et al., 2018; Flueckiger et al., 2015). However, the full potential of associated modelled outputs will only be realised if data are accessed and used to inform local decision making. Recent reviews have suggested that data repositories are mainly targeted toward researchers rather than decision makers and that there is a need to improve indicator data use in low- and middle-income countries (Briand et al., 2018; Omumbo et al., 2013). We describe the development of an open-source web application, MaDD (Malaria Data by District) (Tomlinson et al., 2019), that enables disease distribution data to be more accessible at a local level. The Malaria Atlas Project (MAP) is an international consortium which provides geographical information on diverse aspects of malaria epidemiology (Hay & Snow, 2006). The open-access data generated by MAP have the potential to influence policy at the national and subnational level (Hay & Snow, 2006; Moyes et al., 2013). The project includes sophisticated interpolation models that allow inference of malaria prevalence, as detailed in national and regional indicator surveys, at non-sampled locations (Giorgi et al., 2018; Hay & Snow, 2006). Getting contemporary estimates of malaria metrics to policy makers is essential, but barriers to acceptance exist, notably for modelled predictions; these include the complexity of the statistics described within output reports, and the description of assumptions made during the modelling process (Whitty, 2015). Additional barriers include the sheer wealth of data available, making it difficult to find and choose data surfaces despite central repositories that may be easily navigable. These factors have contributed towards a general lack of modelled outputs being used by local-level implementation programmes in Africa (Omumbo et al., 2013). Most modelled MAP data are provided as spatial estimates, presented as 5 × 5 km gridded surfaces, for example, estimates of Plasmodium falciparum prevalence and mortality, estimates of indoor residual spraying coverage and estimates of dominant vector species distributions and abundance (Bhatt et al., 2015; Gething et al., 2016; Sinka et al., 2016). Though data generated at this spatial resolution provides a visual indication of subnational disparities, it is not immediately clear how these data may be used directly in operational decision-making. For modelled data to be utilised by operational staff at a local level, there is a requirement for additional tools and the ability to convert such data into operationally useful metrics at the level of administrative units (Knight et al., 2016; Omumbo et al., 2013; Whitty, 2015). Data curated by MAP can already be accessed via online interactive maps (Malaria Atlas Project, 2019), an online country profiles tool and the malariaAtlas R package (Pfeffer et al., 2018). These are powerful tools enabling access to MAP generated data that do include data summaries by administrative units. However, because of the wealth of data and functionality it is not straightforward to find and use these tools to perform district-level comparisons. Here, we present an application that allows rapid generation and comparison of summary statistics for a select suite of malaria indicator variables at the sub-national administrative level. MaDD is open-source and coded in R, so it can easily be modified to address local needs (R Core Team, 2019). This is a step towards developing tools for local decision makers to inform questions such as, “where should we prioritise the targeting of IRS rounds this season?”

The Time Local Convex Hull method as a tool for assessing responses of fauna to habitat restoration: A case study using the perentie (Varanus giganteus: Reptilia: Varanidae)

Understanding the behavioural responses of animals to habitat change is vital to their conservation in landscapes undergoing restoration. Studies of animal responses to habitat restoration typically assess species presence/absencehowever, such studies may be restricted in their ability to show whether restoration is facilitating the return of self-sustaining and functional fauna populations. We present a case study using VHF/GPS tracking of a young adult perentie (Varanus giganteus), to demonstrate the range of applications of the Time Local Convex Hull method of home-range construction in analysing the behavioural responses of fauna to habitat change and restoration. Presence/absence studies provide single point locations of an animal, and the Minimum Convex Polygon method provides an invariant estimate of habitat use across the whole home range. However, the Time Local Convex Hull method provides a useful method for assessing movement and behavioural responses of fauna to habitat change and restoration, and the specific habitat requirements for the long-term support of populations. The breadth and multidimensionality of data generated indicates strongly that understanding the complex interactions between animals and their environment is fundamental to their conservation in the face of ever-increasing rates of human-induced habitat change and degradation

CRISPR-Cas9 Causes Chromosomal Instability and Rearrangements in Cancer Cell Lines, Detectable by Cytogenetic Methods

CRISPR-Cas9 has quickly become the method of choice for genome editing, with multiple publications describing technical advances and novel applications. It has been widely adopted as a tool for basic research and has significant translational and clinical potential. However, its usage has outpaced the establishment of essential and rigorous controls for unwanted off-target effects, manifested as small mutations, large deletions of target loci, or large-scale chromosomal rearrangements. A common application of CRISPR-Cas9 is as a tool for creating isogenic cell-line models to study the effects of precise mutations, or variants, on disease traits. Here, we describe the effect of standard CRISPR-Cas9 mutagenesis protocols on well characterized cancer cell lines. We demonstrate that commonly used methods for detecting correctly mutated clones fail to uncover large-scale rearrangements. We show that simple cytogenetic methods can be used to identify clones carrying chromosomal abnormalities and large mutations at target loci. These methods are quick and cost-efficient, and we suggest that such controls should be performed prior to publication of studies based on novel CRISPR-Cas9 mutated cancer cell lines

Clinically relevant enhancement of human sperm motility using compounds with reported phosphodiesterase inhibitor activity

STUDY QUESTION: Can we identify compound(s) with reported phosphodiesterase inhibitor (PDEI) activity that could be added to human spermatozoa in vitro to enhance their motility without compromising other sperm functions? SUMMARY ANSWER: We have identified several compounds that produce robust and effective stimulation of sperm motility and, importantly, have a positive response on patient samples. WHAT IS KNOWN ALREADY: For >20 years, the use of non-selective PDEIs, such as pentoxifylline, has been known to influence the motility of human spermatozoa; however, conflicting results have been obtained. It is now clear that human sperm express several different phosphodiesterases and these are compartmentalized at different regions of the cells. By using type-specific PDEIs, differential modulation of sperm motility may be achieved without adversely affecting other functions such as the acrosome reaction (AR). STUDY DESIGN, SIZE, DURATION: This was a basic medical research study examining sperm samples from normozoospermic donors and subfertile patients attending the Assisted Conception Unit (ACU), Ninewells Hospital Dundee for diagnostic semen analysis, IVF and ICSI. Phase 1 screened 43 commercially available compounds with reported PDEI activity to identify lead compounds that stimulate sperm motility. Samples were exposed (20 min) to three concentrations (1, 10 and 100 µM) of compound, and selected candidates (n = 6) progressed to Phase 2, which provided a more comprehensive assessment using a battery of in vitro sperm function tests.  PARTICIPANTS/MATERIALS, SETTING, METHODS: All healthy donors and subfertile patients were recruited at the Medical Research Institute, University of Dundee and ACU, Ninewells Hospital Dundee (ethical approval 08/S1402/6). In Phase 1, poor motility cells recovered from the 40% interface of the discontinuous density gradient were used as surrogates for patient samples. Pooled samples from three to four different donors were utilized in order to reduce variability and increase the number of cells available for simultaneous examination of multiple compounds. During Phase 2 testing, semen samples from 23 patients attending for either routine diagnostic andrology assessment or IVF/ICSI were prepared and exposed to selected compounds. Additionally, 48 aliquots of prepared samples, surplus to clinical use, were examined from IVF (n = 32) and ICSI (n = 16) patients to further determine the effects of selected compounds under clinical conditions of treatment. Effects of compounds on sperm motility were assessed by computer-assisted sperm analysis. A modified Kremer test using methyl cellulose was used to assess sperm functional ability to penetrate into viscous media. Sperm acrosome integrity and induction of apoptosis were assessed using the acrosomal content marker PSA-FITC and annexin V kit, respectively. MAIN RESULTS AND THE ROLE OF CHANCE: In Phase 1, six compounds were found to have a strong effect on poor motility samples with a magnitude of response of ≥60% increase in percentage total motility. Under capacitating and non-capacitating conditions, these compounds significantly (P ≤ 0.05) increased the percentage of total and progressive motility. Furthermore, these compounds enhanced penetration into a cervical mucus substitute (P ≤ 0.05). Finally, the AR was not significantly induced and these compounds did not significantly increase the externalization of phosphatidylserine (P = 0.6, respectively). In general, the six compounds maintained the stimulation of motility over long periods of time (180 min) and their effects were still observed after their removal. In examinations of clinical samples, there was a general observation of a more significant stimulation of sperm motility in samples with lower baseline motility. In ICSI samples, compounds #26, #37 and #38 were the most effective at significantly increasing total motility (88, 81 and 79% of samples, respectively) and progressive motility (94, 93 and 81% of samples, respectively). In conclusion, using a two-phased drug discovery screening approach including the examination of clinical samples, 3/43 compounds were identified as promising candidates for further study. LIMITATIONS, REASONS FOR CAUTION: This is an in vitro study and caution must be taken when extrapolating the results. Data for patients were from one assessment and thus the robustness of responses needs to be established. The n values for ICSI samples were relatively small. WIDER IMPLICATIONS OF THE FINDINGS: We have systematically screened and identified several compounds that have robust and effective stimulation (i.e. functional significance with longevity and no toxicity) of total and progressive motility under clinical conditions of treatment. These compounds could be clinical candidates with possibilities in terms of assisted reproductive technology options for current or future patients affected by asthenozoospermia or oligoasthenozoospermia

3M_BANTOR: A regression framework for multitask and multisession brain network distance metrics

AbstractBrain network analyses have exploded in recent years and hold great potential in helping us understand normal and abnormal brain function. Network science approaches have facilitated these analyses and our understanding of how the brain is structurally and functionally organized. However, the development of statistical methods that allow relating this organization to phenotypic traits has lagged behind. Our previous work developed a novel analytic framework to assess the relationship between brain network architecture and phenotypic differences while controlling for confounding variables. More specifically, this innovative regression framework related distances (or similarities) between brain network features from a single task to functions of absolute differences in continuous covariates and indicators of difference for categorical variables. Here we extend that work to the multitask and multisession context to allow for multiple brain networks per individual. We explore several similarity metrics for comparing distances between connection matrices and adapt several standard methods for estimation and inference within our framework: standard F test, F test with scan-level effects (SLE), and our proposed mixed model for multitask (and multisession) BrAin NeTwOrk Regression (3M_BANTOR). A novel strategy is implemented to simulate symmetric positive-definite (SPD) connection matrices, allowing for the testing of metrics on the Riemannian manifold. Via simulation studies, we assess all approaches for estimation and inference while comparing them with existing multivariate distance matrix regression (MDMR) methods. We then illustrate the utility of our framework by analyzing the relationship between fluid intelligence and brain network distances in Human Connectome Project (HCP) data

Improving the efficiency of aerosolized insecticide testing against mosquitoes

Developing robust and standardised approaches for testing mosquito populations against insecticides is vital for understanding the effectiveness of new active ingredients or formulations. Methods for testing mosquito susceptibility against contact insecticides or products, such as those delivered through public health programmes, are well-established and standardised. Nevertheless, approaches for testing volatile or aerosolized insecticides used in household products can be challenging to implement efficiently. We adapted WHO guidelines for household insecticides to develop a standardised and higher-throughput methodology for testing aerosolized products in a Peet Grady test chamber (PG-chamber) using caged mosquitoes and an efficient decontamination method. The new approach was validated using insecticide resistant and susceptible Aedes and Anopheles mosquito colonies. An added feature is the inclusion of cage-facing cameras to allow real-time quantification of knockdown following insecticide exposure. The wipe-based decontamination method was highly effective for removing pyrethroids' aerosolized oil-based residues from chamber surfaces, with < 2% mortality recorded for susceptible mosquitoes tested directly on the surfaces. There was no spatial heterogeneity for knockdown or mortality of caged mosquitoes within the PG chamber. The dual-cage approach we implement yields eight-times the throughput compared to a free-flight protocol, allows simultaneous testing of different mosquito strains and effectively discriminates susceptible and resistant mosquito colonies tested side-by-side

Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements.

Wolbachia is a genus of obligate bacterial endosymbionts that infect a diverse range of arthropod species as well as filarial nematodes, with its single described species, Wolbachia pipientis , divided into several ‘supergroups’ based on multilocus sequence typing. Wolbachia strains in mosquitoes have been shown to inhibit the transmission of human pathogens, including Plasmodium malaria parasites and arboviruses. Despite their large host range, Wolbachia strains within the major malaria vectors of the Anopheles gambiae and Anopheles funestus complexes appear at low density, established solely on PCR-based methods. Questions have been raised as to whether this represents a true endosymbiotic relationship. However, recent definitive evidence for two distinct, high-density strains of supergroup B Wolbachia within Anopheles demeilloni and Anopheles moucheti has opened exciting possibilities to explore naturally occurring Wolbachia endosymbionts in Anopheles for biocontrol strategies to block Plasmodium transmission. Here, we utilize genomic analyses to demonstrate that both Wolbachia strains have retained all key metabolic and transport pathways despite their smaller genome size, with this reduction potentially attributable to degenerated prophage regions. Even with this reduction, we confirmed the presence of cytoplasmic incompatibility (CI) factor genes within both strains, with wAnD maintaining intact copies of these genes while the cifB gene was interrupted in wAnM, so functional analysis is required to determine whether wAnM can induce CI. Additionally, phylogenetic analysis indicates that these Wolbachia strains may have been introduced into these two Anopheles species via horizontal transmission events, rather than by ancestral acquisition and subsequent loss events in the Anopheles gambiae species complex. These are the first Wolbachia genomes, to our knowledge, that enable us to study the relationship between natural strain Plasmodium malaria parasites and their anopheline hosts.</jats:p