Biology subjects

King, J.

Publications and source records attributed to King, J..

11 recordsLinked to original sources

bioRxiv2018

Subclonal architecture, evolutionary trajectories and patterns of inheritance of germline variants in pediatric glioblastoma

Pediatric glioblastoma (pGBM) is a lethal cancer with no effective therapies. Intratumoral genetic heterogeneity and mode of tumor evolution have not been systematically addressed for this cancer. Whole-genome sequencing of germline-tumor pairs showed that pGBM is characterized by intratumoral genetic heterogeneity and consequent subclonal architecture. We found that pGBM undergoes extreme evolutionary trajectories, with primary and recurrent tumors having different subclonal compositions. Analysis of variant allele frequencies supported a model of tumor growth involving slow-cycling cancer stem cells that give rise to fast-proliferating progenitor-like cells and to non-dividing cells. pGBM patients germlines had subclonal structural variants, some of which underwent dynamic frequency fluctuations during tumor evolution. By sequencing germlines of mother-father-patient trios, we found that inheritance of deleterious germline variants from healthy parents cooperate with de novo germline and somatic events to the tumorigenic process. Our studies therefore challenge the current notion that pGBM is a relatively homogeneous molecular entity.

cancer biology↗

bioRxiv2018

Gsmodutils: A python based framework for test-driven genome scale metabolic model development

MotivationGenome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include thousands of reactions and metabolites, with many crucial pathways that only become activated in specific simulation settings. However, despite their widespread use, power and the availability of tools to aid with the construction and analysis of large scale models, little methodology is suggested for the continued management of curated large scale models. For example, when genome annotations are updated or new understanding regarding behaviour of is discovered, models often need to be altered to reflect this. This is quickly becoming an issue for industrial systems and synthetic biotechnology applications, which require good quality reusable models integral to the design, build and test cycle.\n\nResultsAs part of an ongoing effort to improve genome scale metabolic analysis, we have developed a test-driven development methodology for the continuous integration of validation data from different sources. Contributing to the open source technology based around COBRApy, we have developed the gsmodutils modelling framework placing an emphasis on test-driven design of models through defined test cases. Crucially, different conditions are configurable allowing users to examine how different designs or curation impact a wide range of system behaviours, minimising error between model versions.\n\nAvailabilityThe software framework described within this paper is open source and freely available from http://github.com/SBRCNottingham/gsmodutils

bioinformatics↗

bioRxiv2018

Non-heritable variation in individual fitness adds stability to neutral theories in ecology and evolution

Neutral theories in ecology1 and evolution2 contend that high diversity of natural communities and high rates of molecular evolution conform to models where individuals have equal fitness and mutations have no effects. Demographic stochasticity makes community and population compositions inherently unstable under these models, with overall levels of diversity being maintained by random processes. This is in contrast with niche and adaptive theories which emphasize differences between species or genotypes as the key to their coexistence3. Here we show that non-heritable variation in individual fitness within species or genotypes can stabilize coexistence without evoking niche differentiation. We construct two classes of mathematical models based on experimental evidence: (1) bacterial growth with variation in cell longevity4,5; and (2) microbial transmission in a host population with variation in host susceptibility6-11. We find stable coexistence of 2 bacterial species in the first model under a single oscillating resource, and 3 or more in the second with independent distributions of host susceptibility to the various microbial species. We discuss the implications of these findings for the interpretation of common measures of relative fitness and for the maintenance of biodiversity.

ecology↗

bioRxiv2018

Human hippocampal theta oscillations reflect sequential dependencies during spatial planning.

Movement-related theta oscillations in rodent hippocampus coordinate forward sweeps of location-specific neural activity that could be used to evaluate spatial trajectories online. This raises the possibility that increases in human hippocampal theta power accompany the evaluation of upcoming spatial choices. To test this hypothesis, we measured neural oscillations during a spatial planning task that closely resembles a perceptual decision-making paradigm. In this task, participants searched visually for the shortest path between a start and goal location in novel mazes that contained multiple choice points, and were subsequently asked to make a spatial decision at one of those choice points. We observed ~4-8 Hz hippocampal/medial temporal lobe theta power increases specific to sequential planning that were negatively correlated with subsequent decision speed, where decision speed was inversely correlated with choice accuracy. These results implicate the hippocampal theta rhythm in decision tree search during planning in novel environments.

neuroscience↗

bioRxiv2018

Two Sides of the Same Coin: The Hippocampus as a Common Neural Substrate for Model-Based Planning and Spatial Memory

Little is known about the neural mechanisms that allow humans and animals to plan actions using knowledge of task contingencies. Emerging theories hypothesize that it involves the same hippocampal mechanisms that support self-localization and memory for locations. Yet, there is limited direct evidence for the link between model-based planning and the hippocampal place map. We addressed this by investigating model-based planning and place memory in healthy controls and epilepsy patients treated using unilateral anterior temporal lobectomy with hippocampal resection. We found that both functions were impaired in the patient group. Specifically, the planning impairment was related to right hippocampal lesion size, controlling for overall lesion size. Furthermore, planning and place memory covaried with one another, but only in neurologically intact controls, consistent with both functions relying on the same structure in the healthy brain. These findings clarify the scope of hippocampal contributions to behavior and the neural mechanism of model-based planning.

neuroscience↗

bioRxiv2018

Kilohertz frame-rate two-photon tomography

Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits imaging speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and uses prior information to recover high-resolution images at over 1.4 billion voxels per second. Using a structural image as a prior for recording neural activity, we imaged visually-evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250 {micro}m and frame-rates over 1 kHz. Dendritic glutamate transients in anaesthetized mice are synchronized within spatially-contiguous domains spanning tens of microns at frequencies ranging from 1-100 Hz. We demonstrate high-speed recording of acetylcholine and calcium sensors, 3D single-particle tracking, and imaging in densely-labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.

neuroscience↗

bioRxiv2018

Achieving the Endgame: Integrated NTD Case Searches

Trachoma and Guinea Worm Disease (GWD) are neglected tropical diseases (NTDs) slated for elimination as a public health problem and eradication respectively by the World Health Organization. As these programs wind down, uncovering the last remaining cases becomes an urgent priority. In 2010, The Ghana Health Service, along with The Carter Center, Sightsavers, and other partners, conducted integrated case search for cases of both GWD and the last stage of trachoma disease, trachomatous trichiasis (TT), as well as providing treatment for trachoma to meet elimination and eradication targets. House to house case search for both diseases was conducted and two case management strategies were explored: a centralized referral to services method and a Point of Care (POC) delivery method. 835 suspected TT cases were discovered in the centralized method, of which 554 accepted surgery. 482 suspected TT cases were discovered in the POC method and all TT cases accepted surgery in the POC searches. The cost per TT case examined was lower in the POC searches compared to the centralized searches ($19.97 in the POC searches and $20.85 in the centralized searches). Both strategies resulted in high surgical uptake for TT surgery, with average uptakes of 72.4% and 83.9% for the centralized and POC searches respectively. We present here that house to house case search offering services at POC are feasible and a potential tool for elimination and eradication programs nearing their end.\n\nAuthor SummaryTrachoma and Guinea Worm Disease (GWD) are neglected tropical diseases (NTDs) slated for elimination as a public health problem and eradication respectively by the World Health Organization. As these programs wind down, uncovering the last remaining cases becomes an urgent priority in order to confirm that eradiation/elimination targets have been reached. Active case searches are one method of finding these last vestiges of disease. Searches for that look for multiple diseases are referred to as integrated searches. We piloted here integrated case searches for GWD and Trachoma with two case management strategies, a referral approach to a central location, and point of care approach (POC). POC approaches can difficult to implement in low resource settings because they require extensive personnel, financial, and logistical, support. However, POC approaches remove one of the biggest barriers to treatment, time spent traveling to a health center, and thus can improve treatment uptake. We found here that integrated active cases searches with a POC case management approach can be implemented in a low resource setting; and improve acceptance and uptake of trachoma examination and trichiasis surgery respectively without costing much more than the referral case management approach.

epidemiology↗

bioRxiv2018

PIKfyve/Fab1 is required for efficient V-ATPase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection

By engulfing potentially harmful microbes, professional phagocytes are continually at risk from intracellular pathogens. To avoid becoming infected, the host must kill pathogens in the phagosome before they can escape or establish a survival niche. Here, we analyse the role of the phosphoinositide (PI) 5-kinase PIKfyve in phagosome maturation and killing, using the amoeba and model phagocyte Dictyostelium discoideum.\n\nPIKfyve plays important but poorly understood roles in vesicular trafficking by catalysing formation of the lipids phosphatidylinositol (3,5)-bisphosphate (PI(3,5)2) and phosphatidylinositol-5-phosphate (PI(5)P). Here we show that its activity is essential during early phagosome maturation in Dictyostelium. Disruption of PIKfyve inhibited delivery of both the vacuolar V-ATPase and proteases, dramatically reducing the ability of cells to acidify newly formed phagosomes and digest their contents. Consequently, PIKfyve- cells were unable to generate an effective antimicrobial environment and efficiently kill captured bacteria. Moreover, we demonstrate that cells lacking PIKfyve are more susceptible to infection by the intracellular pathogen Legionella pneumophila. We conclude that PIKfyve-catalysed phosphoinositide production plays a crucial and general role in ensuring early phagosomal maturation, protecting host cells from diverse pathogenic microbes.\n\nImportanceCells that capture or eat bacteria must swiftly kill them to prevent pathogens from surviving long enough to escape the bactericidal pathway and establish an infection. This is achieved by the rapid delivery of components that produce an antimicrobial environment in the phagosome, the compartment containing the captured microbe. This is essential both for the function of immune cells and for amoebae that feed on bacteria in their environment. Here we identify a central component of the pathway used by cells to deliver antimicrobial components to the phagosome and show that bacteria survive over three times as long within the host if this pathway is disabled. We show that this is of general importance for killing a wide range of pathogenic and non-pathogenic bacteria, and that it is physiologically important if cells are to avoid infection by the opportunistic human pathogen Legionella.

cell biology↗

bioRxiv2017

Nutrient homeostasis and mechanisms related to nutrient retention by wetland macrophytes in a subtropical wetland.

Nutrient homeostasis relates ambient stoichiometric conditions in an environment to the stoichiometry of living entities of the ecosystem. In wetland ecosystems, vegetation can be a large, highly variable and dynamic sink of nutrients. This study investigated stoichiometric homeostasis of dominant emergent and submerged aquatic vegetation (EAV and SAV, respectively) within two treatment flow-ways (FW) of Everglades Stormwater Treatment Area 2 (STA-2). These FW encompass a large gradient in plant nutrient availability. The hypotheses of this study is that wetland vegetation is non-homeostatic relative to ambient nutrients and consequently nutrient resorption will not vary along the nutrient gradient. We developed a framework to investigate how vegetation uptake and resorption of nutrients contribute separately to homeostasis. Overall, the wetland vegetation in this study was non-homeostatic with respect to differential uptake of nitrogen (N) vs. phosphorus (P). Resorption evaluated for EAV was high for P and moderate for N, resorption efficiency did not significantly vary along the gradient and therefore did not affect overall homeostatic status. Nutrient addition experiments may help to compensate for some of the limitation of our study, especially with respect to resolving the primary nutrient source (organic vs. inorganic sources, water vs. soil compartment) and nutrient utilization rates.

ecology↗

bioRxiv2017

Stoichiometric relationships amongst ecosystem compartments of a subtropical treatment wetland

BackgroundEvaluation of carbon (C), nitrogen (N) and phosphorus (P) ratios in aquatic and terrestrial ecosystems can advance our understanding of biological processes, nutrient cycling and the fate of organic matter (OM) in aquatic ecosystems. Eutrophication of aquatic ecosystems can disrupt the accumulation and decomposition of OM which serves as the base of the aquatic food web, and is central to the effectiveness of a treatment wetland. This study investigated nutrient stoichiometry within and between wetland ecosystem compartments (i.e. water column, vegetation, flocculent and soil) of two treatment flow-ways (FWs) in the Everglades Stormwater Treatment Areas located in south Florida (USA). These FWs include an emergent aquatic vegetation cell dominated by Typha spp.(cattail) and a submerged aquatic vegetation cell composed of species such as Chara spp. (muskgrass) and Potamogeton spp. (pondweed). The primary objective of this evaluation was to determine if nutrient stoichiometry is consistent within and between ecosystems and compartments to understand biogeochemical cycling and controls of nutrient removal within a treatment wetland ecosystem.\n\nResultsThis study demonstrates that C, N, and P stoichiometry can be highly variable among ecosystem compartments and between differing wetland ecosystems. Generally, total P declined along the length of each treatment FW in all ecosystem compartments, whereas trends in total N and C trends were more variable. These changes in C and nutrient concentrations result in variable nutrient stoichiometry along treatment FWs signaling potential changes in absolute and relative nutrient availability and biogeochemical processes.\n\nConclusionsAssessment of wetland nutrient stoichiometry between and within ecosystem compartments suggest decoupling of C:N:P relationships likely as a consequence of differential external nutrient supply, differences in primary producer communities and differential decomposition of organic matter. However, stoichiometry varies often monotonous along the flow paths, likely exhibiting a response to nutrient loading. Differences in C:N:P ratios in primary producers, light availability, microbial immobilization in the early stage of decomposition as well as nutrient mining during decomposition of OM are likely feedback mechanisms that lead to deviations from fixed stoichiometry, which in turn may have considerable influence on nutrient removal rates. This information could be used to further understand water treatment performance with respect to stoichiometric processes and OM decomposition.

ecology↗

bioRxiv2017

Novel Magnetic Resonance Imaging strategy targeting Neurotensin Receptors in detection of Prostate Cancer

Prostate cancer is the second leading cause of all male cancer deaths. One of the factors present in malignant prostate cells and shown to support its metastatic growth is the neuropeptide neurotensin (NT). The primary goal of the present study was to establish the feasibility of using a newly developed paramagnetic receptor ligand for NT and non-invasive ultrahigh-field magnetic resonance (MR) imaging to visualize prostate cancer in rodents. Orthotropic xenografts were initiated in six-week old male BALB/c nu/nu athymic mice (n = 28) by intra-prostatic (ventral lobe) inoculation of human prostate cancer cells (10L of PC3 cells (106 /100l)). Palpable tumors developed within 30-60 days. A micro-imager utilized in these studies was an actively shielded 9.4T, 89 mm bore, Oxford superconducting magnet with a 100 gauss/cm gradient system. Prior to contrast injection, T2 weighted anatomy scans were done to localize the tumor with a spin-echo multi-slice sequence with TR: 2000 TE: 40 and NEX: 1 in both coronal and axial planes. The paramagnetic ligand data sets were collected with a spin-echo, T1 weighted pulse sequence (MSME): TR 300 msec; TE 5 msec; NEX 4 in both axial and coronal planes. The data sets were taken initially at 5-min intervals post contrast injection for the first half hour and then at 15 min intervals for the next 1.5-2 hours for a time series analyses. The temporal distribution of MR signal intensity in various regions were determined in the absence and presence of NT. Our results confirm that the novel NT molecule was protected from enzymatic degradation and capable of forming a high affinity paramagnetic NT ligand with an extended half-life. During the imaging studies, the signal intensity increased by 200 % in the region of the tumor. This increase in signal intensity approached maximum binding within 30 minutes and remained visible for 1 hour post-injection of the contrast agent. Taken together, these findings suggest that it is feasible to detect and image prostate cancer using a paramagnetic NT ligand and the emergence of the NT receptor ligand that may be used as a diagnostic marker for prostate cancer in humans.

cancer biology↗