Size Of Subpopulation Research Articles

Design, optimization, and inference of biphasic decay of infectious virus particles.

Virus population dynamics are driven by counter-balancing forces of production and loss. Whereas viral production arises from complex interactions with susceptible hosts, the loss of infectious virus particles is often approximated as a first-order kinetic process. As such, experimental protocols to measure infectious virus loss are not typically designed to identify non-exponential decay processes. Here, we propose methods to evaluate if an experimental design is adequate to identify multiphasic virus particle decay and to optimize the sampling times of decay experiments, accounting for uncertainties in viral kinetics. First, we evaluate synthetic scenarios of biphasic decays, with varying decay rates and initial proportions of subpopulations. We show that robust inference of multiphasic decay is more likely when the faster decaying subpopulation predominates insofar as early samples are taken to resolve the faster decay rate. Moreover, design optimization involving non-equal spacing between observations increases the precision of estimation while reducing the number of samples. We then apply these methods to infer multiple decay rates associated with the decay of bacteriophage ('phage') , an evolved isolate derived from phage . A pilot experiment confirmed that decay is multiphasic, but was unable to resolve the rate or proportion of the fast decaying subpopulation(s). We then applied a Fisher information matrix-based design optimization method to propose non-equally spaced sampling times. Using this strategy, we were able to robustly estimate multiple decay rates and the size of the respective subpopulations. Notably, we conclude that the vast majority (94%) of the phage population decays at a rate 16-fold higher than the slow decaying population. Altogether, these results provide both a rationale and a practical approach to quantitatively estimate heterogeneity in viral decay.

Spatio-temporal metapopulation trends: The coconut crabs of Zanzibar.

Species experience a variety of environmental and anthropogenic conditions across their ranges leading to spatial variation in population dynamics. Understanding population dynamics under different conditions is important but it is challenging to allocate limited effort to spatial and temporal subpopulation monitoring. Using GLMMs, we analyze survey data of a metapopulation of coconut crabs spanning 7 years and 15 sites in and near the Pemba archipelago, Zanzibar, to estimate trends in population size (based on catch per unit effort), weight and sex ratio at the meta- and subpopulation level and investigate anthropogenic drivers of these trends. We found that the overall metapopulation has remained stable in terms of size and composition over the survey period, but observed diverging trends in population size and sex ratio at some subpopulations. Formal protection of sites was associated with positive population trends. Of nine sites for which we could estimate site-specific trends, three showed increasing and two decreasing trends, whereas four sites had stable subpopulations. Although anthropogenic factors affected the average weight, and the incidence of small and large individuals, we found no temporal trends in any weight-related measures. Furthermore, there were no apparent patterns between weight-related measures and subpopulation trends. The metapopulation was biased toward males, and exploitation appeared to be associated with declining trends in the proportion of females, likely an artifact of a strong decline in the proportion of females in one of only two exploited sites in the dataset. Educational campaigns implemented in 2020 at six sites were not related to higher population sizes in later surveys. The variable trends in subpopulation sizes and composition highlight the need for spatially replicated monitoring in metapopulations. The analyses further provide a detailed baseline for future subpopulation studies of this vulnerable species in one of its last remaining metapopulations in the Western Indian Ocean.

Combined demographic, ecological and genetic tools reveal connectivity within a fragmented butterfly population

Protected species require targeted studies to establish population sizes, their dispersal capacity and the possible genetic bottleneck effect that could impair the future of the remaining populations. In this study, we used the genotyping-by-sequencing technique (SNP: single nucleotide polymorphism) combined with Capture-Mark-Recapture (CMR) method to measure the dispersal ability and subpopulation sizes of the protected butterfly Zerynthia polyxena in 14 sites of NW Italian Alps. The study species form a metapopulation divided into several small subpopulations (ranging from 90 to 859 estimated subpopulation sizes). The species showed low mobility, likely due to habitat fragmentation, with individuals travelling an average of 80 m from their original capture site. SNPs highlighted high observed heterozygosity, low genetic substructuring at short distances, and large genetic differentiation only for individuals found in sites located at 46 km distance, suggesting high gene flow at short distances and limited gene flow between distant populations. Although CMR data did not detect movement beyond 700 m, the genetic results revealed remarkable connectivity among nearby subpopulations. The results indicate that gene flow still exists among the subpopulations despite the fragmented habitat. Considering that the species is locally threatened by habitat loss due to the planning of a European high-speed railway, our data suggest that it is not too late to adopt conservation measures. In conclusion, combining genetic and ecological studies can be utilised to design proper conservation plans for protected and threatened insect metapopulations.

Spherical search algorithm with memory-guided population stage-wise control for bound-constrained global optimization problems

The recently proposed Spherical Search (SS) algorithm replaces the traditional square search pattern with a spherical boundary to provide position-diverse solutions. The algorithm balances its exploration and exploitation performance by utilizing 2 exploration and exploitation sub-populations of equal size. SS has been proven to be highly competitive. However, we observed that when it is used to solve a variety of problems as well as during different searching stages, the fixed sub-population size limits its adaptability and flexibility for achieving continuous exploitation–exploration balance. The balance potential of two operators with distinct characteristics is underdeveloped. As a result, SS and its advanced variants are prone to still easily falling into local optima and lacks certain performance advantages over peer algorithms. In this paper, we further develop SS and propose a memory-guided population stage-wise control strategy based SS, called SSM. By our proposed memory-guided stage-wise evaluation mechanism, SS evaluates the exploitation–exploration balance extent in real time and thus adaptively optimizes and predicts better resource allocation ratio values between its 2 sub-populations and thus achieves significant performance advantages over peer algorithms. The experiments are conducted on 120 benchmark functions and 22 real-world problems, and the results show that SSM significantly outperforms other 13 state-of-the-art evolutionary algorithms. Additionally, we conduct analyses based on method characteristics, convergence process, solution quality robustness testing, population diversity, exploitation and exploration balance, and computational complexity.

Abstract 3636: Myeloid cell rebound associated with GD2-CAR-T cell therapy in solid tumor patients

Abstract GD2 is a validated cancer immunotherapy target with highly restricted normal tissue expression. Promising activity of GD2-CAR-T cell therapy in diffuse midline glioma and neuroblastoma has promoted interest in this therapy. We initiated three phase 1 clinical trials of escalating doses of intravenously administered autologous GD2-CAR-T cells in patients with advanced GD2-positive solid tumors. Emerging evidence suggests that CAR-T cells may increase circulating myeloid derived suppressor cells (MDSCs) and that this event may be mediated and/or triggered by CAR-T cell-derived cytokines and chemokines. These findings may help to explain the limited persistence of CAR-T cell therapy in solid tumor patients. Hence, we sought evidence of MDSC generation and secretion of relevant cytokines and chemokines in our clinical trial patients. The CARPETS trial (www.anzctr.org.au: ACTRN12620000622909) recently closed to recruitment after enrolling 12 patients (7 melanoma, 4 colorectal cancer, and 1 sarcoma). No significant adverse events were attributable to CAR-T cell therapy. We opened two other GD2-CAR-T cell therapy trials in 2023: LEVI’S-CATCH (ACTRN12622000675729) in patients with diffuse midline glioma at Sydney Children’s Hospital and KARPOS (ACTRN12622001514796) in adult patients with recurrent glioblastoma at Royal Adelaide Hospital. To date, 3 patients have enrolled to LEVI’S-CATCH with the first patient clearing the dose limiting (DLT) evaluation period. Three patients completed enrolment to the first dose cohort of KARPOS without DLTs. In all CARPETS patients, CAR-T cell expansion, which was measured by by DNA quantitative PCR and flow cytometry, peaked during the 6-week post-CAR-T infusion DLT evaluation period. In 6 CARPETS patients for whom peripheral blood samples were available, we found by flow cytometry, newly formed or increased size of pre-existing subpopulations of non-classical monocytes and/or MDSCs of mononuclear and/or polymorphonuclear class, which peaked at or after the time of peak CAR-T cell expansion. Typically, serum levels of inflammatory cytokines and chemokines such as TNF, IL-6, IL-8, CCL2, GM-CSF, and CXCL10, were detected only after the CAR-T cell infusion with variable patterns of the timing and concentration of analyte observed among the 12 patients. At the time of writing, blood samples from the first KARPOS patient showed CAR-T cell expansion and the subsequent increases in circulating myeloid derived suppressor cells and inflammatory cytokines. We expect that full data sets for these parameters will be presented for current and future enrolled patients to both studies. To improve CAR-T cell persistence in solid tumor patients, these data indicate the need for new therapeutic strategies to mitigate effects of CAR-T cell induced myeloid cells with antitumor activity. Citation Format: Michael P. Brown, Tessa Gargett, Nga T. Truong, Orazio Vittorio, David S. Ziegler. Myeloid cell rebound associated with GD2-CAR-T cell therapy in solid tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3636.

Abstract 5452: AXIN2 differentially modulates stem cell subpopulations providing a potential therapeutic opportunity for targeting colorectal cancer stem cells

Abstract Constitutively activated WNT-signaling promotes stem cell (SC) overpopulation which drives most colorectal cancer (CRC) development. It is not known, however, how WNT-signaling activity regulates different SC sub-populations. We previously reported that SC population size decreases as AXIN2 is knocked down, and increases when AXIN2 is overexpressed. Changes in cell cycle and apoptotic rate were also observed. Here, we present our recent results on changes between different SC subpopulations (ALDH+ vs. LGR5+) that occur due to AXIN2 modulation. We hypothesize that modulation of AXIN2 promotes differential expansion between different CRC SC subpopulations (ALDH+ and LGR5+). We observed that AXIN2 not only increases LGR5+ SC population size, but also expands the ALDH+ SC population to a greater extent as shown by an increased ALDH+-to-LGR5+ SCs ratio. This indicates that AXIN2, via WNT signaling, regulates SC population size, particularly ALDH+ SCs. Since the ALDH SC marker is also a key component in the retinoic acid (RA) signaling pathway, we surmised that increased AXIN2 would not only lead to elevated ALDH levels, but also upregulate the RA-signaling pathway components in CRC cells. To this end, we conducted NanoString mRNA profiling to study the effects of AXIN2 knockdown and overexpression in HT29 and SW480 CRC cells. The results showed that increased AXIN2 significantly up-regulated several key components of the RA-signaling pathway. Taken together, our results indicate that AXIN2 drives a shift in SC subpopulation sizes favoring the ALDH+ SCs. It also promotes the RA-signaling component expression - a pathway known to regulate SC differentiation. As a potential treatment strategy for CRC, therapeutically inducing high levels of AXIN2 could shift the balance between SC populations towards ALDH+ SCs, which may provide a way to target cancer SCs with retinoids to induce their differentiation. Citation Format: Chi Zhang, Caroline O. Facey, Lynn M. Opdenaker, Bruce M. Boman. AXIN2 differentially modulates stem cell subpopulations providing a potential therapeutic opportunity for targeting colorectal cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5452.

Impact of population size on epidemic spreading in a bipartite metapopulation network with recurrent mobility

The mobility pattern of a population plays a key role in the spread of epidemics. Despite extensive work on epidemic spreading, little attention has been paid to the impact of subpopulation size. This paper investigates the spread of epidemics on a bipartite metapopulation network considering recurrent mobility patterns and different sizes of subpopulations. With the Markovian process approach, the epidemic threshold can be predicted as a function of subpopulation size and epidemic parameters. Simulation and theoretical results indicate that there exists a critical mobility intensity below which the epidemic will be eliminated, while limiting the size of the subpopulation can suppress the epidemic. Additionally, the epidemic threshold will approach zero when the size of the public area is large. The results can help the prevention of epidemic spreading under recurrent crowd mobility.

On multi-type Cannings models and multi-type exchangeable coalescents

A multi-type neutral Cannings population model with migration and fixed subpopulation sizes is analyzed. Under appropriate conditions, as all subpopulation sizes tend to infinity, the ancestral process, properly time-scaled, converges to a multi-type coalescent sharing the exchangeability and consistency property. The proof gains from coalescent theory for single-type Cannings models and from decompositions of transition probabilities into parts concerning reproduction and migration respectively. The following section deals with a different but closely related multi-type Cannings model with mutation and fixed total population size but stochastically varying subpopulation sizes. The latter model is analyzed forward and backward in time with an emphasis on its behavior as the total population size tends to infinity. Forward in time, multi-type limiting branching processes arise for large population size. Its backward structure and related open problems are briefly discussed.

Macrophage subpopulation identity in Drosophila is modulated by apoptotic cell clearance and related signalling pathways.

In Drosophila blood, plasmatocytes of the haemocyte lineage represent the functional equivalent of vertebrate macrophages and have become an established in vivo model with which to study macrophage function and behaviour. However, the use of plasmatocytes as a macrophage model has been limited by a historical perspective that plasmatocytes represent a homogenous population of cells, in contrast to the high levels of heterogeneity of vertebrate macrophages. Recently, a number of groups have reported transcriptomic approaches which suggest the existence of plasmatocyte heterogeneity, while we identified enhancer elements that identify subpopulations of plasmatocytes which exhibit potentially pro-inflammatory behaviours, suggesting conservation of plasmatocyte heterogeneity in Drosophila. These plasmatocyte subpopulations exhibit enhanced responses to wounds and decreased rates of efferocytosis when compared to the overall plasmatocyte population. Interestingly, increasing the phagocytic requirement placed upon plasmatocytes is sufficient to decrease thesize of these plasmatocyte subpopulations in the embryo. However, the mechanistic basis for this response was unclear. Here, we examine how plasmatocyte subpopulations are modulated by apoptotic cell clearance (efferocytosis) demands and associated signalling pathways. We show that loss of the phosphatidylserine receptor Simu prevents an increased phagocytic burden from modulating specific subpopulation cells, while blocking other apoptotic cell receptors revealed no such rescue. This suggests that Simu-dependent efferocytosis is specifically involved in determining fate of particular subpopulations. Supportive of our original finding, mutations in amo (the Drosophila homolog of PKD2), a calcium-permeable channel which operates downstream of Simu, phenocopy simu mutants. Furthermore, we show that Amo is involved in the acidification of the apoptotic cell-containing phagosomes, suggesting that this reduction in pH may be associated with macrophage reprogramming. Additionally, our results also identify Ecdysone receptor signalling, a pathway related to control of cell death during developmental transitions, as a controller of plasmatocyte subpopulation identity. Overall, these results identify fundamental pathways involved in the specification of plasmatocyte subpopulations and so further validate Drosophila plasmatocytes as a heterogeneous population of macrophage-like cells within this important developmental and immune model.

A reinforcement learning-based neighborhood search operator for multi-modal optimization and its applications

In this paper, a reinforcement learning-based neighborhood search operator (RLNS) is proposed for multi-modal optimization problems where the main novelties lie in the reinforcement learning-based neighborhood range selection strategy, the neighborhood subpopulation generation strategy and the local vector encirclement model. The reinforcement learning-based neighborhood range selection strategy is proposed to dynamically adjust the subpopulation size to address the issue of too many parameters to be adjusted in the multi-modal optimization algorithm based on the niching methods, while the neighborhood subpopulation generation strategy and the local vector encirclement model are designed with the hope of enhancing the individual’s ability to local exploitation to obtain more accurate solutions. To verify the effectiveness of the proposed RLNS, SSA-RLNS, PSO-RLNS and EO-RLNS are proposed by integrating the proposed RLNS with the existing sparrow search algorithm, particle swarm optimization and equilibrium optimizer. The performances of the proposed SSA-RLNS, PSO-RLNS, EO-RLNS and existing multi-modal optimization algorithms are tested in CEC2015 multi-niche benchmark functions. The experimental results show that the SSA-RLNS, PSO-RLNS and EO-RLNS could locate multiple global optimal solutions with satisfactory accuracy, which illustrate that the proposed RLNS could be successfully used to deal with multi-modal optimization problems by integrating with common population-based optimization algorithms. Finally, the SSA-RLNS is successfully applied in the inverse kinematics of robot manipulator.

A Species-based Particle Swarm Optimization with Adaptive Population Size and Deactivation of Species for Dynamic Optimization Problems

Population clustering methods, which consider the position and fitness of individuals to form sub-populations in multi-population algorithms, have shown high efficiency in tracking the moving global optimum in dynamic optimization problems. However, most of these methods use a fixed population size, making them inflexible and inefficient when the number of promising regions is unknown. The lack of a functional relationship between the population size and the number of promising regions significantly degrades performance and limits an algorithm’s agility to respond to dynamic changes. To address this issue, we propose a new species-based particle swarm optimization with adaptive population size and number of sub-populations for solving dynamic optimization problems. The proposed algorithm also benefits from a novel systematic adaptive deactivation component that, unlike the previous deactivation components, adapts the computational resource allocation to the sub-populations by considering various characteristics of both the problem and the sub-populations. We evaluate the performance of our proposed algorithm for the Generalized Moving Peaks Benchmark and compare the results with several peer approaches. The results indicate the superiority of the proposed method.

Estimating appropriate mowing timing for the population of an endangered butterfly inhabiting grassland patches in an agricultural landscape

It has been recognized that the timing of disturbance, in addition to its intensity and frequency, is important for the population dynamics of organisms because the impact of the disturbance depends on the life history stage at which it occurs (i.e., egg, larva, or adult). However, the effects of disturbance timing on consumer population dynamics have not been explored. This study simultaneously estimated the effects of mowing frequency and timing on the subpopulation dynamics of the endangered grassland butterfly, Plebejus argyrognomon. A two-year investigation of a metapopulation of P. argyrognomon consisting of approximately 150 habitat patches revealed that subpopulation size decreased with increasing mowing frequency, in addition to the positive effect of patch area and habitat connectivity. With the mowing frequency fixed at once per year, subpopulation size maximized when mowing occurred during the adult period in the previous generation, presumably due to reduced impact in the high-mobility adult stage. By mowing during this period, subpopulation size was maintained at several times higher than mowing during the larval period. It is suggested that disturbance timing should be incorporated into the conservation of metapopulations in human-managed landscapes.Implications for insect conservationReducing mowing frequency is important for the conservation of P. argyrognomon. In addition, mowing during the adult stage is best suited for maintaining subpopulations.

A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance.

The use of an antibiotic may lead to the emergence and spread of bacterial strains resistant to this antibiotic. Experimental and theoretical studies have investigated the drug dose that minimizes the risk of resistance evolution over the course of treatment of an individual, showing that the optimal dose will either be the highest or the lowest drug concentration possible to administer; however, no analytical results exist that help decide between these two extremes. To address this gap, we develop a stochastic mathematical model of bacterial dynamics under antibiotic treatment. We explore various scenarios of density regulation (bacterial density affects cell birth or death rates), and antibiotic modes of action (biostatic or biocidal). We derive analytical results for the survival probability of the resistant subpopulation until the end of treatment, the size of the resistant subpopulation at the end of treatment, the carriage time of the resistant subpopulation until it is replaced by a sensitive one after treatment, and we verify these results with stochastic simulations. We find that the scenario of density regulation and the drug mode of action are important determinants of the survival of a resistant subpopulation. Resistant cells survive best when bacterial competition reduces cell birth and under biocidal antibiotics. Compared to an analogous deterministic model, the population size reached by the resistant type is larger and carriage time is slightly reduced by stochastic loss of resistant cells. Moreover, we obtain an analytical prediction of the antibiotic concentration that maximizes the survival of resistant cells, which may help to decide which drug dosage (not) to administer. Our results are amenable to experimental tests and help link the within and between host scales in epidemiological models.

Meta‐ and subpopulation estimation with disparate data: coconut crabs in the Western Indian Ocean

AbstractWidely dispersed fragmented populations are a challenge to monitor because subpopulation sizes may be very small, difficult to access and time consuming to sample regularly. We use the coconut crab (Birgus latro) on Pemba, United Republic of Zanzibar as a case study for estimating highly fragmented populations and metapopulation sizes. The species is a very large terrestrial decapod threatened by exploitation and habitat alteration and now classified as vulnerable. We developed an integrated model to analyse capture‐mark‐recapture (CMR) data from five sites jointly with count data from 24 sites to estimate site‐level densities and population sizes, predicted total population size across the Pemba archipelago, and investigated the effect of six predictors of human influence on density. We fitted separate models to test the effect of the same predictors on raw counts and individual body mass. We estimate the total population of coconut crabs on the Pemba archipelago to be c. 6700 terrestrial individuals. We show that government protection generally affects crabs positively, whereas presence of agriculture negatively affects their densities. This study highlights that time‐consuming CMR data can be leveraged to estimate densities on less visited sites, and that fully protected islands are critical for maintaining relatively high population densities. Our overall population estimate suggests that Pemba still hosts a viable coconut crab population in a part of its range where the species is otherwise in steep decline.

Evaluation of the genetic viability of metapopulation scenarios for the Iberian lynx

AbstractThe Iberian lynx has shown a favourable demographic trajectory in the last decade as a result of the conservation measures adopted which are still ongoing. However, the viability of the species is still compromised by genetic factors. Here, we used the GESP software that predicts the effective population size (Ne) and inbreeding accumulation (∆f) over time in metapopulations, to find realistic scenarios that guarantee the genetic viability of this species. We proposed as genetic targets that Ne of the metapopulation (NeMeta) should exceed 500 in 20 generations (long term), whereas ∆f of the subpopulations (∆fx) should not exceed 0.05 in five generations (short term). The current Iberian lynx metapopulation configuration, with the expected subpopulations sizes at carrying capacity (5 subpops.; Ne1 = 100, Ne2,3,4,5 = 25), does not reach the long‐term goal, with a NeMeta ~ 150 in 20 generations. The results indicate that the long‐term genetic viability of the metapopulation requires an increase in the subpopulation size of 50–200%, the creation of at least 8 new subpopulations, and migration rates close to 0.1 between neighbouring subpopulations, comprising 2165 effective individuals (ca. 1100 breeding females). In addition, a minimum migration rate of 0.05 into the smallest subpopulations of Ne = 25 (i.e. 1.25 migrants/generation) is needed to avoid excessive inbreeding accumulation (short‐term goal). Larger subpopulations are preferable to several smaller subpopulations with the same number of effective individuals, even when the latter are well connected. Although these requirements seem challenging to achieve in the short‐medium term, the study provides key information for informed decision making by environmental managers and policymakers. The conclusions drawn here apply to other carnivores in need of conservation.

Population genetics: coalescence rate and demographic parameters inference

Inferring the demographic history of species is a great challenge in population genetics. This history is classically represented as a history of size changes, ignoring population structure. We present here the work carried out over the last decade around the concept of IICR (Inverse Instantaneous Coalescence Rate), which makes it possible to link, on the one hand, the history of the true population size for a panmictic population, and the inferred size, sometimes called "effective size", when structure is taken into account. We show that population structure can lead to misinterpretations of some demographic history inference results, we propose a framework for inferring structure-specific demographic parameters (number and size of subpopulations, migration rates), and we analyze the link between IICR and some form of selection modeling on genetic sequences.

Waiting times in a branching process model of colorectal cancer initiation

We study a multi-stage model for the development of colorectal cancer from initially healthy tissue. The model incorporates a complex sequence of driver gene alterations, some of which result in immediate growth advantage, while others have initially neutral effects. We derive analytic estimates for the sizes of premalignant subpopulations, and use these results to compute the waiting times to premalignant and malignant genotypes. This work contributes to the quantitative understanding of colorectal tumor evolution and the lifetime risk of colorectal cancer.

Abstract 3805: Revealing the role of microRNAs in the emergence of cancer stem cell heterogeneity during colorectal cancer progression

Abstract Our goal is to identify microRNAs (miRNAs) that target mRNAs involved in stem cell (SC) signaling pathways involved in colorectal cancer (CRC) tumorigenesis. SC overpopulation drives CRC progression but exact mechanism is unclear. Hypothesis: specific miRNAs target SC genes, which leads to the emergence of multiple cancer SC (CSC) sub-populations and tumor heterogeneity. We used flow cytometry to identify CSC sub-populations based on expression of SC markers including ALDH1, LGR5 and others in the HT-29 CRC cell line. CSC sub-populations were isolated and measured using FACS and expression of miRNAs in each CSC sub-population was quantified using NanoString profiling. The level of miRNA upregulation in each CSC sub-population was ranked based on differential expression of the miRNAs between different CSC sub-populations. We chose to further analyze the LGR5 and ALDH SC sub-populations because they showed: i) the largest difference between CSC sub-population sizes, ii) the smallest size (<1%) of the co-positive (LGR5+/ALDH+) cell sub-population, iii) the highest numbers of differentially expressed miRNAs. Note that WNT signaling mainly occurs via LGR5+ CSC and retinoic acid (RA) signaling mainly occurs via ALDH+ CSCs. We report herein miRNAs that are differentially expressed between ALDH+/LGR5- compared to ALDH-/LGR5- subpopulation and LGR5+/ALDH- versus ALDH-/LGR5-. The mRNAs expressed in CSC subpopulations identified from Nanostring profiling were analyzed using bioinformatics for their predicted binding by upregulated miRNAs. Our findings show that: 1) multiple CSC subpopulations exist in the HT-29 cell population; 2) each CSC subpopulation has a unique miRNA signature. Notably, RXRA mRNA is significantly upregulated in the ALDH+/LGR5- CSC sub-population but not in the LGR5+/ALDH- CSC subpopulation. We identified 5 miRs upregulated in the LGR5+/ALDH- CSC subpopulation that are predicted to target the 3’UTR of RXRA mRNA. One of these miRs, miR-660-3p, is specifically upregulated in the LGR5+/ALDH- CSC subpopulation and binding of miR-660-3p to RXRA mRNA was validated using luciferase assay in HT-29 cells. We previously reported that RXRA is selectively expressed in ALDH + CSC sub-populations. Also, RXRA is known to bind with β-catenin leading to its degradation and suppression of WNT-based transcriptional activity. Taken together, these results indicate that expression of miR-660-3p, by inhibiting RXRA expression, increases WNT signaling and decreases RA signaling in LGR5+/ALDH- CSCs. Thus, upregulated miR-660-3p targets a key gene in the RA signaling pathway (RXRA) which could contribute to the emergence of SC sub-populations during CRC development. Citation Format: Molly Lausten, Victoria Stark, Caroline Facey, Lynn Opdenaker, Bruce M. Boman. Revealing the role of microRNAs in the emergence of cancer stem cell heterogeneity during colorectal cancer progression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3805.

Effects of Simulated Gastrointestinal Conditions on Combined Potentially Probiotic Limosilactobacillus fermentum 296, Quercetin, and/or Resveratrol as Bioactive Components of Novel Nutraceuticals.

This study evaluated the effects of simulated gastrointestinal conditions (SGIC) on combined potentially probiotic Limosilactobacillus fermentum 296 (~ 10 log CFU/mL), quercetin (QUE, 160mg), and/or resveratrol (RES, 150mg) as the bioactive components of novel nutraceuticals. Four different nutraceuticals were evaluated during exposure to SGIC and analyzed the plate counts and physiological status of L. fermentum 296, contents and bioaccessibility of QUE and RES, and antioxidant capacity. Nutraceuticals with QUE and RES had the highest plate counts (4.94 ± 0.32 log CFU/mL) and sizes of live cell subpopulations (28.40 ± 0.28%) of L. fermentum 296 after SGIC exposure. An index of injured cells (Gmean index, arbitrary unit defined as above 0.5) indicated that part of L. fermentum 296 cells could be entered the viable but nonculturable state when the nutraceuticals were exposed to gastric and intestinal conditions while maintaining vitality. The nutraceuticals maintained high contents (QUE ~ 29.17 ± 0.62 and RES ~ 23.05mg/100g) and bioaccessibility (QUE ~ 41.0 ± 0.09% and RES ~ 67.4 ± 0.17%) of QUE and RES, as well as high antioxidant capacity (ABTS assay ~ 88.18 ± 1.16% and DPPH assay 75.54 ± 0.65%) during SGIC exposure, which could be linked to the protective effects on L. fermentum 296 cells. The developed nutraceuticals could cross along the gastrointestinal tract with high concentrations of functioning potentially probiotic cells and bioavailable phenolic compounds to exert their beneficial impacts on consumer health, being an innovative strategy for the co-ingestion of these bioactive components.

Camera‐trapping density estimates suggest critically low population sizes for the Wet Tropics subspecies of the spotted‐tailed quoll (Dasyurus maculatus gracilis)

AbstractAccurate estimates of distribution and population density are critical for the management of threatened species. This is particularly pertinent for mammalian predators, whose generally low population density, elusive nature, and large home range requirements make it difficult to detect declines. We aimed to refine population estimates of the northern spotted‐tailed quoll (Dasyurus maculatus gracilis) in the Wet Tropics bioregion, to estimate the total number of adults, the likely size of subpopulations across the known distribution of the subspecies, and its associated conservation status. We performed targeted upland camera‐trapping surveys from June 2017 to May 2019. To calculate population densities, we used a combination of the number of individuals identified from each survey and the mean maximum distance moved from three life history stages. We then extrapolated these estimates to modelled suitable habitat areas, refined by the camera‐trapping surveys. Population sizes for the six defined subpopulations were estimated, and ranged from approximately 5 to 105 individuals. The total population was estimated to be 221 individuals. This total population estimate, and the estimates for each of the subpopulations, are lower than previous published estimates and are cause for concern. Given the low population estimates presented here and unresolved threats driving declines in some subpopulations, we suggest elevation of this subspecies to Critically Endangered under the EPBC Act.