Biology subjects

Moore, J.

Publications and source records attributed to Moore, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2020

Microstructural characterization and validation of a 3D printed phantom for diffusion MRI

PurposeTo introduce and characterize inexpensive and easily produced 3D-printed axon-mimetic (3AM) diffusion MRI (dMRI) phantoms in terms of pore geometry and diffusion kurtosis imaging (DKI) metrics. MethodsPhantoms were 3D-printed with a composite printing material that, after dissolution of the PVA, exhibits microscopic fibrous pores. Confocal microscopy and synchrotron phase contrast micro-CT imaging were performed to visualize and assess the pore sizes. dMRI scans of four identical phantoms and phantoms with varying print parameters in water were performed at 9.4T. DKI was fit to both datasets and used to assess the reproducibility between phantoms and effects of print parameters on DKI metrics. Identical scans were performed 25 and 76 days later to test their stability. ResultsSegmentation of pores in three microscopy images yielded a mean, median, and standard deviation of equivalent pore diameters of 7.57 m, 3.51 m, and 12.13 m, respectively. Phantoms with identical parameters showed a low coefficient of variation ([~]10%) in DKI metrics (D=1.38 x10-3 mm2/s and K=0.52, T1= 3960 ms and T2=119 ms). Printing temperature and speed had a small effect on DKI metrics (<16%) while infill density had a larger and more variable effect (>16%). The stability analysis showed small changes over 2.5 months (<7%). Conclusion3AM phantoms can mimic the fibrous structure of axon bundles on a microscopic scale, serving as complex, anisotropic dMRI phantoms.

neuroscience↗

bioRxiv2020

Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis

Recent advances in genetics have increased our understanding of epistasis as important in the genetics of complex phenotypes. However, current analytical methods often cannot detect epistasis, given the multiple testing burden. To address this, we extended our previous method, Evolutionary Triangulation (ET), that uses differences among populations in both disease prevalence and allele frequencies to filter SNPs from association studies to generate novel interaction models. We show that two-locus ET identified several co-evolving gene pairs, where both genes associate with the same disease, and that the number of such pairs is significantly greater than expected by chance. Traits found by two-locus ET included those related to pigmentation and schizophrenia. We then applied two-locus ET to the analysis of preterm birth (PTB) genetics. Using ET to filter SNPs at loci identified by genome-wide association studies (GWAS), we showed that ET derived PTB two-locus models are novel and were not seen when only the index SNPs were used to generate epistatic models. One gene pair, ADCY5 and KCNAB1 5’, was identified as significantly interacting in a model of gestational age (p as low as 3 × 10−3). Notably, the same ET SNPs in these genes showed significant interactions in three of four cohorts analyzed. The robustness of this gene pair and others, demonstrated that the ET method can be used without prior biological hypotheses based on SNP function to select variants for epistasis testing that could not be identified otherwise. Two-locus ET clearly increased the ability to identify epistasis in complex traits.View Full Text

genetics↗

bioRxiv2020

Development of a Coronavirus Disease 2019 Nonhuman Primate Model Using Airborne Exposure

Airborne transmission is predicted to be a prevalent route of human exposure with SARS-CoV-2. Aside from African green monkeys, nonhuman primate models that replicate airborne transmission of SARS-CoV-2 have not been investigated. A comprehensive and comparative evaluation of COVID-19 in African green monkeys, rhesus macaques, and cynomolgus macaques following airborne exposure to SARS-CoV-2 was performed to define parameters critical to disease progression and the extent to which they correlate with human COVID-19. Respiratory abnormalities and viral shedding were noted for all animals, indicating successful infection. Cynomolgus macaques developed fever, and thrombocytopenia was measured for African green monkeys and rhesus macaques. Type II pneumocyte hyperplasia and alveolar fibrosis were more frequently observed in lung tissue from cynomolgus macaques and African green monkeys. The data indicate that, in addition to African green monkeys, macaques can be successfully infected by airborne SARS-CoV-2, providing viable macaque natural transmission models for medical countermeasure evaluation. One Sentence SummaryNonhuman primates develop COVID-19 following airborne virus exposure.

microbiology↗

bioRxiv2020

A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.

genomics↗

bioRxiv2020

Elevated soluble Galectin-3 as a marker of chemotherapy efficacy in Breast cancer patients: a prospective study

PurposeGalectin-3 (Gal-3) is a glycan-binding lectin with a debated role in cancer progression due to its various functions and patterns of expression. The current study investigates the relationship between breast cancer prognosis and secreted Gal-3. MethodsBreast cancer patients with first time cancer diagnosis and no prior treatment (n=88) were placed in either adjuvant or neoadjuvant setting based on their treatment modality. Stromal and plasma Gal-3 levels were measured in each patient at the time of diagnosis and then throughout treatment using immunohistochemistry (IHC) and ELISA respectively. Healthy women (>18 years of age, n=63) were used to establish baseline levels of plasma Gal-3. Patients were followed for 84 months for disease free survival analysis. ResultsEnhanced levels of plasma (adjuvant) and stromal (neo-adjuvant) Gal-3 were found to be markers of chemotherapy efficacy. The patients with chemotherapy induced increase in extracellular Gal-3 had longer disease-free interval and significantly lower rate of recurrence during 84-month follow-up compared to patients with unchanged or decreased secretion. ConclusionThe findings support the use of plasma Gal-3 as a marker for chemotherapy efficacy when no residual tumor is visible through imaging. Furthermore, stromal levels in any remaining tumors post chemotherapy can also be used to predict long term prognosis in patients. Key pointsIncreased Gal-3 secretion due to chemotherapy leads to better prognosis and longer disease-free survival. The analysis of soluble Gal-3 expression could be useful as a support tool in predicting treatment efficacy in patients with no visible tumor remaining for follow up through imaging.

cancer biology↗

bioRxiv2019

Tubulin recycling limits cold tolerance

Although cold temperatures have long been used to depolymerize microtubules, how temperature specifically affects the polymerization and depolymerization activities of tubulin proteins and how these lead to changes in microtubule networks in cells has not been established. We investigated these questions in budding yeast, an organism found in diverse environments and therefore predicted to exhibit dynamic microtubules across a broad range of temperatures. We measured the dynamics of GFP-labeled microtubules in living cells and found that lowering the temperature from 37{degrees}C to 10{degrees}C decreased the rates of both polymerization and depolymerization, decreased the amount of polymer assembled before catastrophes and decreased the frequency of microtubule emergence from nucleation sites. Lowering to 4{degrees}C caused rapid loss of almost all microtubule polymer. We provide evidence that these effects on microtubule dynamics may be explained in part by changes in the co-factor-dependent conformational dynamics of tubulin proteins. Ablation of tubulin-binding co-factors further sensitizes cells and their microtubules to low temperatures, and we highlight a specific role for TBCB/Alf1 in microtubule maintenance at low temperatures. Finally, we show that inhibiting the maturation cycle of tubulin by using a point mutant in {beta}-tubulin confers hyper-stable microtubules at low temperatures, rescues the requirement for TBCB/Alf1, and improves the cold tolerance of the yeast. Together, these results reveal an unappreciated step in the tubulin cycle in cells and suggest that this step may be a key limiting factor in the thermal tolerance of organisms.

cell biology↗

bioRxiv2019

Community Standards for Open Cell Migration Data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited due to the diversity of experimental protocols and non-standardised output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardised data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardisation efforts by the Cell Migration Standardisation Organization, CMSO, an open community-driven organisation to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools, and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.

bioinformatics↗

bioRxiv2018

SUCCESSFUL DEMONSTRATION OF ASSISTED GENE FLOW IN THE THREATENED CORAL ACROPORA PALMATA ACROSS GENETICALLY-ISOLATED CARIBBEAN POPULATIONS USING CRYOPRESERVED SPERM

Global change will compromise the population sizes, species ranges, and survival of economically-important plants and animals, including crops, aquaculture species, and foundational ecosystem builders. Scleractinian reef-building corals are a particular concern because they are slow-growing, long-lived, environmentally-sensitive, and concentrated in the warmest regions of the ocean. Assisted Gene Flow (AGF) is considered a viable tool to help natural plant and animal populations, including corals, adapt to changing environments. Our goal was to test for the first time whether cryopreserved coral sperm could be used to facilitate assisted gene flow between genetically-isolated populations of a Caribbean coral. We collected, pooled, and cryopreserved coral sperm from the threatened Caribbean coral Acropora palmata in the western Caribbean (Key Largo, FL), central Caribbean (Rincon, Puerto Rico), and eastern Caribbean (Curacao). Alongside freshly-collected sperm from Curacao, the cryopreserved sperm from each of these populations was used for in vitro fertilization experiments with freshly-collected eggs from Curacao. Across five egg donors, average fertilization success was 91 to 99% for CUR x CUR (fresh sperm) crosses, 37 to 82% for CUR x CUR (frozen sperm) crosses, 3 to 19% for CUR x FL (frozen sperm) crosses and 0 to 24% for CUR x PR (frozen sperm) crosses. Notably, fertilization was achieved in all four categories of crosses, showing for the first time through direct evidence that populations of A. palmata are reproductively compatible, and that genetic diversity can be transferred from one population to another for the purposes of assisted gene flow. The resulting larvae were reared in Curacao for up to 7 days, then the swimming larvae were transported to Florida for settlement and grow-out at two separate facilities, which achieved larval settlement rates of 37 to 60% across all cohorts. Larvae were reared and settled in Florida to acclimate them to the ambient water quality, microbial environment, and temperature regimes of the western genetic A. palmata population as early in their life cycle as possible. At one month, over 54% all settlers had survived, including over 3500 settlers from CUR x CUR (frozen sperm), 1200 settlers from CUR x FL (frozen sperm), and 230 settlers from CUR x PR (frozen sperm). These experiments represent the first-ever pan-Caribbean coral crosses produced in captivity and the first direct evidence that geographically-separated and genetically-isolated populations of any Caribbean coral are reproductively compatible. Moreover, with over 4700 A. palmata settlers produced using cryopreserved sperm, this represents the largest living wildlife population ever created from cryopreserved material. Together, these findings demonstrate that cryopreservation of coral sperm can enable efficient, large-scale assisted gene flow in corals. This form of assisted migration can not only help to preserve the population-level genetic diversity of extant coral populations but also help to increase population resilience to global change.

zoology↗

bioRxiv2018

Geometry alone influences stem cell differentiation in a precision 3D printed stem cell niche

Stem cells within epithelial tissues reside in anatomical structures known as crypts that are known to contribute to the mechanical and chemical milieu important for function. To date, epithelial stem cell therapies have largely ignored the niche and focussed solely on the cell population to be transplanted. Our aim was to recreate the precise geometry of the epithelial stem cell niche using two photon polymerisation and to determine the influence of this structure alone on stem cell phenotype. We were able to recreate crypt structures and following cell seeding, a zonation in cell phenotype along the z-axis emerged. This illustrates that geometry alone, without the use of exogenous signalling molecules, influences cell response. Understanding the role of geometry in the regulation of the stem cell niche will enable significant advances in our ability to influence stem cell behaviour to expedite cellular therapies to the clinic.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/489773v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@152d03eorg.highwire.dtl.DTLVardef@1e5b6ecorg.highwire.dtl.DTLVardef@4c6c02org.highwire.dtl.DTLVardef@14726a5_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

bioengineering↗

bioRxiv2018

A unified model for microtubule rescue

How microtubules transition from depolymerization to polymerization, known as rescue, is poorly understood. Here we examine two models for rescue: 1) an end-driven model in which the depolymerizing end stochastically switches to a stable state; and 2) a lattice-driven model in which rescue-sites are integrated into the microtubule prior to depolymerization. We test these models using a combination of computational simulations and in vitro experiments with purified tubulin. Our findings support the lattice-driven model by identifying repeated rescue sites in microtubules. In addition, we discover an important role for divalent cations in determining the frequency and location of rescue sites. We use wash-in experiments to show that divalent cations inhibit rescue during depolymerization, but not during the polymerization. We propose a unified model in which rescues are driven by embedded rescue sites in microtubules, but the activity of these sites is influenced by changes in the depolymerizing ends.

cell biology↗

bioRxiv2018

TUBA1A mutations identified in lissencephaly patients dominantly disrupt neuronal migration and impair dynein activity

Tubulinopathies are severe human brain malformations associated with mutations in tubulin genes. Despite the identification of many tubulin mutations in patients, we do not understand how these mutations impact the microtubule cytoskeleton, how the changes to microtubule function lead to brain malformations, or how different tubulin isotypes regulate microtubules to support normal neurodevelopment. TUBA1A -tubulin is the most commonly affected tubulin isotype in tubulinopathy patients. Heterozygous mutations in TUBA1A have been identified in patients with diverse cortical malformations including microlissencephaly, lissencephaly, pachygyria, and polymicrogyria. Here we focus on mutations affecting the conserved arginine at position 402 (R402), which account for 30% of all reported TUBA1A mutations in patients. We demonstrate that exogenous expression of TUBA1A-R402C and TUBA1A-R402H patient alleles is sufficient to dominantly disrupt cortical neuron migration in the developing mouse brain, recapitulating the human lissencephaly phenotype. Intriguingly, ectopic expression of TUBA1A-R402C/H alleles does not alter morphology, axonal trafficking, or microtubule polymerization rates in cultured neurons, but does lead to subtle changes in axonal microtubule orientation. Further, we find that budding yeast -tubulin with analogous R402C and R402H mutations assembles into microtubules but disrupts the activity of the microtubule motor dynein. The level of dynein impairment scales with abundance of R402 mutant -tubulin in the cell. Together, our results support a model in which tubulinopathy mutations at R402 poison the microtubule network in young neurons by creating defective binding sites for dynein at the microtubule surface.

developmental biology↗

bioRxiv2018

A Fixed Moderate-dose Combination of Tiletamine+Zolazepam Outperforms Midazolam in Induction of Short-term Immobilization of Ball Pythons (Python regius)

Laboratory animals are commonly anesthetized to prevent pain and distress and to provide safe handling. Anesthesia procedures are well-developed for common laboratory mammals, but not as well established in reptiles. We assessed the performance of intramuscularly injected tiletamine (dissociative anesthetic) and zolazepam (benzodiazepine sedative) in fixed combination (2 mg/kg and 3 mg/kg) in comparison to 2 mg/kg of midazolam (benzodiazepine sedative) in ball pythons (Python regius). We measured heart and respiratory rates and quantified induction parameters (i.e., time to loss of righting reflex, time to loss of withdrawal reflex) and recovery parameters (i.e., time to regain righting reflex, withdrawal reflex, normal behavior). Mild decreases in heart and respiratory rates (median decrease of <10 beats per minute and <5 breaths per minute) were observed for most time points among all three anesthetic dose groups. No statistically significant difference between the median time to loss of righting reflex was observed among animals of any group (p = 0.783). However, the withdrawal reflex was lost in all snakes receiving 3mg/kg of tiletamine+zolazepam but not in all animals of the other two groups (p = 0.0004). In addition, the time for animals to regain the righting reflex and resume normal behavior was longer in the drug combination dose groups compared to the midazolam group (p = 0.0055). Our results indicate that midazolam is an adequate sedative for ball pythons but does not suffice to achieve reliable immobilization or anesthesia, whereas tiletamine+zolazepam achieves short-term anesthesia in a dose-dependent manner.

zoology↗

bioRxiv2018

Validation of a library of cGMP-compliant human pluripotent stem cell lines for use in liver therapy

Recent advancements in the production of hepatocytes from human pluripotent stem cells (hPSC-Heps) afford tremendous possibilities for treatment of patients with liver disease. Validated current good manufacturing practice (cGMP) lines are an essential prerequisite for such applications but have only recently been established. Whether such cGMP lines are capable of hepatic differentiation is not known. To address this knowledge gap, we examined the proficiency of three recently derived cGMP lines (two hiPSC and one hESC) to differentiate into hepatocytes and their suitability for therapy. hPSC-Heps generated using a chemically defined four-step hepatic differentiation protocol uniformly demonstrated highly reproducible phenotypes and functionality. Seeding into a 3D PEG-DA fabricated inverted colloid crystal (ICC) scaffold converted these immature progenitors into more advanced hepatic tissue structures. Hepatic constructs could also be successfully encapsulated into the immune-privileged material alginate. This is the first report we are aware of demonstrating cGMP-compliant hPSCs can generate cells with advanced hepatic function potentially suitable for future therapeutic applications.

cell biology↗

bioRxiv2018

Endogenous protection from ischemic brain injury by preconditioned monocytes

Exposure to low dose lipopolysaccharide prior to cerebral ischemia is neuroprotective in stroke models, a phenomenon termed preconditioning. While it is well established that lipopolysaccharide-preconditioning induces central and peripheral immune responses, the cellular mechanisms modulating ischemic injury remain unclear. Here, we investigated the role of immune cells in the brain protection afforded by preconditioning and we tested whether monocytes may be reprogrammed by ex vivo lipopolysaccharide exposure thus modulating the inflammatory injury after cerebral ischemia in male mice. We found that systemic injection of low-dose lipopolysaccharide induces a distinct subclass of CD115+Ly6Chi monocytes that protect the brain after transient middle cerebral artery occlusion in mice. Remarkably, adoptive transfer of monocytes isolated from preconditioned mice into naive mice 7 hours after transient middle cerebral artery occlusion reduced brain injury. Gene expression and functional studies showed that IL-10, iNOS and CCR2 in monocytes are essential for the neuroprotection. This protective activity was elicited even if mouse or human monocytes were exposed ex vivo to lipopolysaccharide and then injected into male mice after stroke. Cell tracking studies showed that protective monocytes are mobilized from the spleen and reach brain and meninges, wherein they suppressed post-ischemic inflammation and neutrophils influx into the brain parenchyma. Our findings unveil a previously unrecognized subpopulation of splenic monocytes capable to protect the brain with an extended therapeutic window, and provide the rationale for cell therapies based on the delivery of autologous or allogeneic protective monocytes into patients with ischemic stroke.\n\nSignificance StatementInflammation is a key component of the pathophysiology of the brain in stroke, a leading cause of death and disability with limited therapeutic options. Here, we investigate endogenous mechanisms of protection against cerebral ischemia. Using LPS preconditioning as an approach to induce ischemic tolerance in mice, we found the generation of neuroprotective monocytes within the spleen from where they traffic to the brain and meninges suppressing post-ischemic inflammation. Importantly, systemic LPS preconditioning can be mimicked by adoptive transfer of in vitro-preconditioned mouse or human monocytes at translational relevant time points after stroke. This model of neuroprotection may facilitate clinical efforts to increase the efficacy of bone marrow mononuclear cell treatments in acute neurological diseases such as cerebral ischemia.

neuroscience↗

bioRxiv2017

Transcriptome-wide analysis of the functional intronome using spliceosome profiling

Full understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA-Seq provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-Seq alone to reveal the full repertoire of spliced species. Here we present \"spliceosome profiling\", a strategy based on deep sequencing of RNAs co-purifying with late stage spliceosomes. Spliceosome profiling allows for unambiguous mapping of intron ends to single nucleotide resolution and branchpoint identification at unprecedented depths. Our data reveal hundreds of new introns in S. pombe and numerous others that were previously misannotated. By providing a means to directly interrogate sites of spliceosome assembly and catalysis genome-wide, spliceosome profiling promises to transform our understanding of RNA processing in the nucleus much like ribosome profiling has transformed our understanding mRNA translation in the cytoplasm.

genomics↗

bioRxiv2017

A Feed-forward Relay between Bicoid and Orthodenticle Regulates the Timing ofEmbryonic Patterning in Drosophila

The K50 homeodomain (K50HD) protein Orthodenticle (Otd) is critical for anterior patterning and brain and eye development in most metazoans. In Drosophila melanogaster, another K50HD protein, Bicoid (Bcd), has evolved to replace Otds ancestral function in embryo patterning. Bcd is distributed as a long-range maternal gradient and activates transcription of a large number of target genes including otd. Otd and Bcd bind similar DNA sequences in vitro, but how their transcriptional activities are integrated to pattern anterior regions of the embryo is unknown. Here we define three major classes of enhancers that are differentially sensitive to binding and transcriptional activation by Bcd and Otd. Class 1 enhancers are initially activated by Bcd, and activation is transferred to Otd via a feed-forward relay (FFR) that involves sequential binding of the two proteins to the same DNA motif. Class 2 enhancers are activated by Bcd, and maintained by an Otd-independent mechanism. Class 3 enhancers are never bound by Bcd, but Otd binds and activates them in a second wave of zygotic transcription. The specific activities of enhancers in each class are mediated by DNA motif variants preferentially bound by Bcd or Otd, and the presence or absence of sites for cofactors that interact with these proteins. Our results define specific patterning roles for Bcd and Otd, and provide mechanisms for coordinating the precise timing of gene expression patterns during embryonic development.

molecular biology↗

bioRxiv2017

The structured demography of open populations in fluctuating environments

At the spatial scale relevant to many field studies and management policies, populations may experience more external recruitment than internal recruitment. These sources of recruitment, as well as local demography, are often subject to stochastic fluctuations in environmental conditions. Here, we introduce a class of stochastic models accounting for these complexities and provide analytic methods for understanding their long-term behavior. The population state n(x) of these stochastic models is a function or vector keeping track of densities of individuals with continuous (e.g. size) or discrete (e.g. age) traits x taking values in a compact metric space. This state variable is updated by a stochastic affine equation nt+1 = At+1nt + bt+1 where At+1 is a time varying operator (e.g. an integral operator or a matrix) that updates the local demography, and bt+1 is a time varying function or vector representing external recruitment. When the realized per-capita growth rate of the local demography is negative, we show that all initial conditions converge to the same time-varying trajectory. Furthermore, when A1, A2... and b1, b2, ... are stationary sequences, this limiting behavior is determined by a unique stationary distribution. When the stationary sequences are periodic, uncorrelated, or a mixture of these two types of stationarity, we derive explicit formulas for the mean, within-year covariance, and auto-covariance of the stationary distribution. Sensitivity formulas for these statistical features are also given. The analtyic methods are illustrated with applications to discrete size-structured models of space-limited coral populations, and continuously size-structured models of giant clam populations.

ecology↗

bioRxiv2017

Restoration of Eastern oyster populations with positive density dependence

AO_SCPCAPBSTRACTC_SCPCAPPositive density dependence can create a threshold of population states below which extinction of the population occurs. The existence of this threshold, which can often be a complex, multi-dimensional surface, rather than a single point, is of particular importance in degraded populations for which there is a desire for successful restoration. Here, we incorporated positive density dependence into a closed, size- and age-structured integral projection model parameterized with empirical data from an Eastern oyster, Crassostrea virginica, population in Pamlico Sound, North Carolina. To understand the properties of the threshold surface, and implications for restoration, we introduced a general method based on a linearization of the threshold surface at its unique, unstable equilibrium. We estimated the number of oysters of a particular age (i.e. stock enhancement), or the surface area of hard substrate required (i.e. habitat enhancement), to move a population from an extinction trajectory to a persistent trajectory. The location of the threshold surface was strongly affected by changes in the amount of local larval retention. Traditional stock enhancement with oysters less than a year old (i.e. spat) required three times as many oysters relative to stock enhancement with oysters between ages three and seven, while the success of habitat enhancement depended upon the initial size distribution of the population. The methodology described here demonstrates the importance of considering positive density dependence in oyster populations, and also provides insights into effective management and restoration strategies when dealing with a high dimensional threshold separating extinction and persistence.

ecology↗