Biology subjects

Evans, M.

Publications and source records attributed to Evans, M..

28 records · Page 2Linked to original sources

bioRxiv2020

Individual Differences in the Connectivity of Left and Right Anterior Temporal Lobes Relate to Modality and Category Effects in Semantic Categorisation

Contemporary neuroscientific accounts suggest that ventral anterior temporal lobe (ATL) regions act as a bilateral heteromodal semantic hub. However, research also shows graded functional differences between the hemispheres relating to linguistic versus non-linguistic semantic tasks and to knowledge of objects versus people. Individual differences in connectivity from bilateral ATL and between left and right ATL might therefore give rise to differences in function within this system. We investigated whether the relative strength of intrinsic connectivity from left and right ATL would relate to differences in performance on semantic tasks. We examined resting-state fMRI in 74 individuals and, in a separate session, examined semantic categorisation, manipulating stimulus type (famous faces versus landmarks) and modality of presentation (visual versus verbal). We found that people with greater connectivity between left and right ATL were more efficient at categorising landmarks, especially when these were presented visually. In addition, participants who showed stronger connectivity from right than left ATL to medial occipital cortex showed more efficient semantic categorisation of landmarks regardless of modality of presentation. These findings show that individual differences in the intrinsic connectivity of left and right ATL are associated with effects of category and modality in semantic categorisation. The results can be interpreted in terms of graded differences in the strengths of inputs from spoke regions, such as regions of visual cortex, to a bilateral yet partially segregated semantic hub, encompassing left and right ATL.

neuroscience↗

bioRxiv2020

Contrasting population genetics of cattle- and buffalo- derived Theileria annulata causing tropical theileriosis

The present study was designed to improve understanding of Theileria annulata in sympatric water buffalo and cattle in the Punjab province of Pakistan. The prevalence of tropical theileriosis is high, buparvaquone resistance is widespread, and vaccine protection is poor in the field. Better understanding is, therefore, needed of the factors that influence the genetics of T. annulata populations both within its hosts and in its overall populations. Here we utilise a panel of six satellites and a mitochondrial cytochrome b marker to explore the multiplicity of T. annulata infection and patterns of emergence and spread of different parasite genotypes. Parasite materials were collected from infected animals in defined regions, where water buffalo and cattle are kept together. Our results show that T. annulata is genetically more diverse in cattle- than in water buffalo-derived populations (the mean numbers of unique satellite alleles were 13.3 and 1.8 and numbers of unique cytochrome b locus alleles were 65 and 27 in cattle- and water buffalo-derived populations, respectively). The data show a high level of genetic diversity among the individual host-derived populations (the overall heterozygosity (He) indices were 0.912 and 0.931 in cattle, and 0.874 and 0.861 in buffalo, based on satellite and cytochrome b loci, respectively). When considered in the context of high parasite transmission rates and frequent animal movements between different regions, the predominance of multiple T. annulata genotypes, with multiple introductions of infection in the hosts from which the parasite populations were derived, may have practical implications for the spread of parasite genetic adaptations; such as those conferring vaccine cross-protection against different strains affecting cattle and buffalo, or resistance to antiprotozoal drugs.

genetics↗

bioRxiv2019

On the use of calcium deconvolution algorithms in practical contexts

Calcium imaging is a powerful tool for capturing the simultaneous activity of large populations of neurons. Here we determine the extent to which our inferences of neural population activity, correlations, and coding depend on our choice of whether and how we deconvolve the calcium time-series into spike-driven events. To this end, we use a range of deconvolution algorithms to create nine versions of the same calcium imaging data obtained from barrel cortex during a pole-detection task. Seeking suitable values for the deconvolution algorithms parameters, we optimise them against ground-truth data, and find those parameters both vary by up to two orders of magnitude between neurons and are sensitive to small changes in their values. Applied to the barrel cortex data, we show that a substantial fraction of the processing methods fail to recover simple features of population activity in barrel cortex already established by electrophysiological recordings. Raw calcium time-series contain an order of magnitude more neurons tuned to features of the pole task; yet there is also qualitative disagreement between deconvolution methods on which neurons are tuned to the task. Finally, we show that raw and processed calcium time-series qualitatively disagree on the structure of correlations within the population and the dimensionality of its joint activity. Collectively, our results show that properties of neural activity, correlations, and coding inferred from calcium imaging are sensitive to the choice of if and how spike-evoked events are recovered. We suggest that quantitative results obtained from population calcium-imaging be verified across multiple processed forms of the calcium time-series.

neuroscience↗

bioRxiv2019

Novel metabarcoded DNA sequencing tool for the detection of Plasmodium species in malaria positive patients

Various PCR based methods have been described for the diagnosis of malaria, but most depend on the use of Plasmodium species-specific probes and primers; hence only the tested species are identified and there is limited available data on the true circulating species diversity. Sensitive diagnostic tools and platforms for their use are needed to detect Plasmodium species in both clinical cases and asymptomatic infections that contribute to disease transmission. We have been recently developed for the first time a novel high throughput haemoprotobiome metabarcoded DNA sequencing method and applied it for the quantification of haemoprotozoan parasites (Theleria and Babesia) of livestock. Here, we describe a novel, high throughput method using an Illumina MiSeq platform to demonstrate the proportions of Plasmodium species in metabarcoded DNA samples derived from human malaria patients. Plasmodium falciparum and Plasmodium vivax positive control gDNA was used to prepare mock DNA pools of parasites to evaluate the detection threshold of the assay for each of the two species and to assess the accuracy of proportional quantification. We then applied the assay to malaria-positive human samples to show the species composition of Plasmodium communities in the Punjab province of Pakistan and in the Afghanistan-Pakistan tribal areas. The diagnostic performance of the deep amplicon sequencing method was compared to an immunochromatographic assay that is widely used in the region. Metabarcoded DNA sequencing showed better diagnostic performance, greatly increasing the estimated prevalence of Plasmodium infection. The next-generation sequencing method using metabarcoded DNA has potential applications in the diagnosis, surveillance, treatment, and control of Plasmodium infections, as well as to study the parasite biology.

genetics↗

bioRxiv2019

Evidence for reduced CTX-M carriage in cattle-associated Escherichia coli at low temperatures and on publicly accessible farmland: implications for surveillance and potential for farm-to-human transmission

Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g. CTX-M {square}-lactamase-positive Escherichia coli). Here, we collected samples, monthly over a two-year period, on 53 dairy farms in the South West of England, and data for 610 variables concerning antimicrobial usage, management practices and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin streptomycin and tetracycline, respectively, in 2754/4145 (66%), 263/4145 (6%), 1475/4145 (36%) and 2874/4145 (69%) of all samples from faecally contaminated sites. E. coli positive for blaCTX-M were detected in 224/4145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibiotic dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with increased odds of blaCTX-M positivity. Low temperature was associated with reduced odds of blaCTX-M E. coli positivity in samples and to reduced odds of finding E. coli resistant to each of the four test antibacterials. This was additional to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had increased odds of having E. coli resistance to each antibacterial or positive for blaCTX-M. Samples collected on pastureland had reduced odds of having E. coli resistant to amoxicillin or tetracycline, and being positive for blaCTX-M. ImportanceAntibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including to track the impacts of interventions aimed at reducing the prevalence of resistance. In this epidemiological survey of dairy farm antibacterial resistance, we show that local temperature, as it changes over the course of a year, is associated with the prevalence of antibacterial resistant E. coli. Also, that prevalence of resistant E. coli is higher in indoor environments and in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time-point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm with regard to the presence or number of resistant E. coli.

microbiology↗

bioRxiv2019

A system for tracking whisker kinematics and whisker shape in three dimensions

Quantification of behaviour is essential for systems neuroscience. Since the whisker system is a major model system for investigating the neural basis of behaviour, it is important to have methods for measuring whisker movements from behaving animals. Here, we developed a high-speed imaging system that measures whisker movements simultaneously from two vantage points. We developed an algorithm that uses the stereo video data to track multiple whiskers by fitting 3D curves to the basal section of each target whisker. By using temporal information to constrain the fits, the algorithm is able to track multiple whiskers in parallel with low error rate. We used the output of the tracker to produce a 3D description of each tracked whisker, including its 3D orientation and 3D shape, as well as bending-related mechanical force. In conclusion, we present an automatic system to track whiskers in 3D from high-speed video, creating the opportunity for comprehensive 3D analysis of sensorimotor behaviour and its neural basis.\n\nAuthor summaryThe great ethologist Niko Tinbergen described a crucial challenge in biology to measure the \"total movements made by the intact animal\". Advances in high-speed video and machine analysis of such data have made it possible to make profound advances. Here, we target the whisker system. The whisker system is a major experimental model in neurobiology and, since the whiskers are readily imageable, the system is ideally suited to machine vision. Rats and mice explore their environment by sweeping their whiskers to and fro. It is important to measure whisker movements in 3D, since whiskers move in 3D and since the mechanical forces that act on them are 3D. However, the problem of automatically tracking whiskers in 3D from video has generally been regarded as prohibitively difficult. Our innovation here is to extract 3D information about whiskers using a two-camera, high-speed imaging system and to develop computational methods to infer 3D whisker state from the imaging data. Our hope is that this study will facilitate comprehensive, 3D analysis of whisker behaviour and, more generally, contribute new insight into brain mechanisms of perception and behaviour.

neuroscience↗

bioRxiv2019

Development of a deep amplicon sequencing method to determine the proportional species composition of piroplasm haemoprotozoa as an aid in their control

Piroplasmosis is caused by tick-borne haemoprotozoa of the genera Theileria and Babesia. These parasitic infections can cause serious impact on the health of livestock and production. Multiple piroplasm species can infect a single host, but reliable molecular diagnostic tools are needed with which to understand the composition of these complex parasite communities. Theileria and Babesia vary in their epidemiology, drug sensitivity, pathogenicity and interaction of co-infecting species, but are similar in the animals, become persistent carriers after recovery from primary infection, acting as reservoir hosts. Here, we describe for the first time the use of a deep amplicon sequencing platform to identify proportions of piroplasm species in co-infecting communities and develop the concept of a \"haemoprotobiome\". First, four phenotypically-verified species of Theileria and Babesia were used to prepare mock pools with random amounts of the parasites and amplified with four different numbers of PCR cycles to assess sequence representation of each species. Second, we evaluated the detection threshold of the deep amplicon sequencing assay for each of the four species and to assess the accuracy of proportional quantification of all four species. Finally, we applied the assay to the field samples to afford insight of the species composition of piroplasm communities in small and large ruminants in the Punjab province of Pakistan. The \"haemoprotobiome\" concept has several potential applications in veterinary and human research, including understanding of responses to drug treatment; parasite epidemiology and ecology; species interactions during mixed infections; and parasite control strategies.

microbiology↗

bioRxiv2019

Development of high throughput methods for the analysis of anthelmintic resistance allele frequencies in field populations of gastrointestinal nematodes.

Drug resistant helminths have become a major cause of poor health and production in sheep and goats, and there is a need for diagnostic markers and tools to determine the frequency of resistance alleles in field parasite populations. Gastrointestinal nematode resistance to benzimidazole drugs is caused by a mutation in one of three positions on the isotype 1 {beta}-tubulin locus, and in the absence of markers for resistance to other broad spectrum anthelmintic classes, these provide a relevant study example. Determination of the prevalence of these single nucleotide polymorphisms in field gastrointestinal nematode populations can be impractical using conventional molecular methods, which may be error prone or lack sensitivity at low levels of resistance. Here, we report the development of a novel method based on an Illumina Mi-seq deep amplicon sequencing platform; to sequence the isotype 1 {beta}-tubulin locus of the small ruminant gastrointestinal nematode, Teladorsagia circumcincta, and determine the frequency of the benzimidazole resistance mutations. We validated the method by assessing sequence representation bias in the isotype 1 {beta}-tubulin locus, comparing the results of Illumina Mi-seq and pyrosequencing, and applying the method to populations containing known proportions of resistant and susceptible L3. Finally, we applied the method to field samples collected from ewes and lambs on over a period of one year on three farms, each highlighting different aspects of sheep management and approaches to parasite control. The results show opportunities to build hypotheses with reference to selection pressures leading to differences in resistance allele frequencies between sampling dates, farms and ewes or lambs, and to consider the impact of their genetic fixation or otherwise. This study provides proof of concept of a practical, accurate, sensitive and scalable method to determine frequency of anthelmintic drug resistance mutations in gastrointestinal nematodes in field studies and as a management tool for livestock farmers.

molecular biology↗

bioRxiv2018

Rapid sensing of L-leucine by human and murine hypothalamic neurons: neurochemical and mechanistic insights

ObjectiveDietary proteins are sensed by hypothalamic neurons and strongly influence multiple aspects of metabolic health, including appetite, weight gain and adiposity. However, little is known about the mechanisms by which hypothalamic neural circuits controlling behavior and metabolism sense protein availability. The aim of this study is to characterize how neurons from the mediobasal hypothalamus respond to a signal of protein availability: the amino acid L-leucine.\n\nMethodsWe used primary cultures of post-weaning murine mediobasal hypothalamic neurons, hypothalamic neurons derived from human induced pluripotent stem cells, and calcium imaging to characterize rapid neuronal responses to physiological changes in extracellular L-Leucine concentration.\n\nResultsA neurochemically diverse subset of both mouse and human hypothalamic neurons responded rapidly to L-leucine. Consistent with L-leucines anorexigenic role, we found that 25% of mouse MBH POMC neurons were activated by L-leucine. 10% MBH NPY neurons were inhibited by L-leucine, and leucine rapidly reduced AGRP secretion, providing a mechanism for the rapid leucine-induced inhibition of foraging behaviour in rodents. Surprisingly, none of the candidate mechanisms previously implicated in hypothalamic leucine sensing (KATP channels, mTORC1 signaling, amino-acid decarboxylation) were involved in the acute activity changes produced by L-leucine. Instead, our data indicate that leucine-induced neuronal activation involves a plasma membrane Ca2+ channel, whereas leucine-induced neuronal inhibition is mediated by inhibition of a store-operated Ca2+ current.\n\nConclusionsA subset of neurons in the mediobasal hypothalamus rapidly respond to physiological changes in extracellular leucine concentration. Leucine can produce both increases and decreases in neuronal Ca2+ concentrations in a neurochemically-diverse group of neurons, including some POMC and NPY/AGRP neurons. Our data reveal that leucine can signal through novel mechanisms to rapidly affect neuronal activity.\n\nHighlights- A neurochemically diverse group of mouse and human hypothalamic neurons rapidly sense and respond to L-leucine\n- Leucine can produce neuronal activation or neuronal inhibition via distinct and novel Ca2+ signaling mechanisms.\n- Leucine activates 25% ARH POMC neurons\n- Leucine inhibits 10% ARH NPY/AGRP neurons and reduces AGRP secretion from fasted mediobasal hypothalamic slices

neuroscience↗

bioRxiv2017

Targeting regulatory T cells with Interleukin-2 treatment in type 1 diabetes: a response-adaptive, non-randomised, open-label trial of repeat doses of Aldesleukin (DILfrequency)

BackgroundType 1 diabetes (T1D) results from loss of immune regulation leading to the development of autoimmunity to pancreatic beta-cells, involving autoreactive T effector cells (Teffs). Regulatory T cells (Tregs), that prevent autoimmunity, require Interleukin-2 (IL-2) for maintenance of immunosuppressive functions and, alterations in the IL-2 pathway predispose to T1D. Using an adaptive trial design we aimed to determine the optimal regimen of aldesleukin (recombinant human IL-2) to physiologically enhance Tregs while limiting expansion of autoreactive Teffs.\n\nMethodsDILfrequency is a single-center, non-randomised, open-label, response-adaptive study of participants aged 18 to 70 years with T1D. The initial learning phase allocated 12 participants to six different predefined dose-frequency regimens. Then, three cohorts of 8 participants were sequentially allocated dose-frequencies, based on repeated interim analyses of all accumulated trial data. The co-primary endpoints were percentage change in Tregs, Teffs and, CD25 ( subunit of the IL-2 receptor) expression by Tregs, from baseline to steady state. Trial registration ISRCTN40319192 and ClinicalTrials.gov (NCT02265809).\n\nFindings115 participants were assessed between November 17th 2014 and May 22nd 2016, 38 participants were enrolled with 36 completing treatment. The optimal regimen to maintain a steady state increase in Tregs of 30% and CD25 expression of 25% without Teff expansion is 0.26 x 106 IU/m2 (95% CI (-0.007 to 0.485)) every 3 days (1.3 to 4.4). Tregs and CD25 were dose-frequency responsive, while Teffs were not. The commonest adverse event was injection site reaction (464/694 events), with a single participant developing transient eosinophilia at the highest dose (0.47 x 106 IU/m2).\n\nInterpretationThis response-adaptive trial defined a well-tolerated aldesleukin regimen that specifically induces Treg expansion that can now be trialled to treat T1D.\n\nFundingSir Jules Thorn Trust, Wellcome, JDRF, SNSF, NIHR

clinical trials↗