Bayesian spatial modeling of moose count data: increasing estimator efficiency and exploring ecological hypotheses

Moose management throughout much of Alaska and Canada relies on aerial count data, which are commonly collected using the geospatial population estimator (GSPE) protocol. The GSPE uses a model-based analytical approach and finite-population block kriging to estimate abundance from a collection of sampled survey units. Widespread implementation and well-documented analytical software have resulted in reliable estimates of moose abundance, density, and composition across a large proportion of their range. Analysis is conducted almost exclusively using the GSPE software, which fits a fixed model structure to data collected within a single year. The downside of this approach to analysis is that the fixed model structure is inefficient for estimation, leading to more field effort than would otherwise be necessary to achieve a desired level of estimator precision. We developed a more easily modified and flexible Bayesian spatial general additive model approach (BSG) that accommodates spatial and temporal covariates (e.g., habitat characteristics, trend), multiple survey events, prior information, and incomplete detection. Using a series of 6 GSPE surveys conducted in Yukon-Charley Rivers National Preserve, Alaska, USA, from 2003–2019, we established the equivalence of the 2 approaches under similar model structures. We then extended the BSG to demonstrate how a more comprehensive approach to analysis can affect estimator precision and be used to assess ecological relationships. The precision of annual abundance estimators from the BSG were improved by an average of 43% over those based on the standard GSPE analysis, highlighting the very real costs of assuming a fixed (i.e., suboptimal) model structure. The population increased at a rate of 2.3%/year (95% CrI = 0.8–3.8%), and the increase was largely explained by a parallel increase in wildfire extent (i.e., high quality moose habitat). These results suggest that our approach could be used to increase estimator efficiency or decrease future survey costs without any modifications to the basic protocol. While modification of the GSPE software is possible, practitioners may find the BSG approach more convenient for quickly developing model structures for a particular application, thereby allowing them to extract more information from existing and future datasets.     

Localization of the human NCAM gene to band q23 of chromosome 11: the third gene coding for a cell interaction molecule mapped to the distal portion of the long arm of chromosome 11

cDNA clones containing sequences coding for the murine neural cell adhesion molecule (N-CAM) were used in Southern hybridizations on human genomic DNA and demonstrated approximately 90% homology between human and murine NCAM genes. In situ hybridization with one of these clones was performed on human metaphase chromosomes and allowed the localization of the human NCAM gene to band q23 of chromosome 11. The genes for two other cell surface molecules believed to be involved in cell-cell interactions, Thy-1 and the delta chain of the T3-T cell receptor complex, have recently been localized to the same region of chromosome 11 in man. Moreover, this region of the human chromosome 11 appears to be syntenic to a region of murine chromosome 9 that also contains the staggerer locus: staggerer mice show abnormal neurological features which may be related to abnormalities in the conversion of the embryonic to the adult forms of the N-CAM molecule.     

Increased nonsterol isoprenoids, dolichol and ubiquinone, in the Smith-Lemli-Opitz syndrome: effects of dietary cholesterol

Smith-Lemli-Opitz syndrome (SLOS) is an inherited autosomal recessive cholesterol deficiency disorder. Our studies have shown that in SLOS children, urinary mevalonate excretion is normal and reflects hepatic HMG-CoA reductase activity but not ultimate sterol synthesis. Hence, we hypothesized that in SLOS there may be increased diversion of mevalonate to nonsterol isoprenoid synthesis. To test our hypothesis, we measured urinary dolichol and ubiquinone, two nonsterol isoprenoids, in 16 children with SLOS and 15 controls, all fed a low-cholesterol diet. The urinary excretion of both dolichol (P < 0.002) and ubiquinone (P < 0.02) in SLOS children was 7-fold higher than in control children, whereas mevalonate excretion was comparable. In a subset of 12 SLOS children, a high-cholesterol diet decreased urinary mevalonate excretion by 61% (P < 0.001), dolichol by 70% (P < 0.001), and ubiquinone by 67% (P < 0.03). Our hypothesis that in SLOS children, normal urinary mevalonate excretion results from increased diversion of mevalonate into the production of nonsterol isoprenoids is supported. Dietary cholesterol supplementation reduced urinary mevalonate and nonsterol isoprenoid excretion but did not change the relative ratios of their excretion. Therefore, in SLOS, a secondary peripheral regulation of isoprenoid synthesis may be stimulated.     

T cell phenotypes in women with Chlamydia trachomatis infection and influence of treatment on phenotype distributions

T cell phenotypes involved in the immune response to Chlamydia trachomatis (CT) have not been fully elucidated in humans. We evaluated differences in T cell phenotypes between CT-infected women and CT-seronegative controls and investigated changes in T cell phenotype distributions after CT treatment and their association with reinfection. We found a higher expression of T cell activation markers (CD38⁺HLA-DR⁺), T helper type 1 (Th1)- and Th2-associated effector phenotypes (CXCR3⁺CCR5⁺ and CCR4⁺, respectively), and T cell homing marker (CCR7) for both CD4⁺ and CD8⁺ T cells in CT-infected women. At follow-up after treatment of infected women, there were a lower proportion of CD4⁺ and CD8⁺ T cells expressing these markers. These findings suggest a dynamic interplay of CD4⁺ and CD8⁺ T cells in CT infection, and once the infection is treated, these cell markers return to basal expression levels. In women without reinfection, a significantly higher proportion of CD8⁺ T cells co-expressing CXCR3 with CCR5 or CCR4 at follow-up was detected compared to women with reinfection, suggesting they might play some role in adaptive immunity. Our study elucidated changes in T cell phenotypes during CT infection and after treatment, broadening our understanding of adaptive immune mechanisms in human CT infections.     

Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.     

BCNU-induced protection from hyperbaric hyperoxia: role of glutathione metabolism

To explore the role of the glutathione oxidation-reduction cycle in altering the sensitivity of rats to the effects of hyperbaric hyperoxia, we administered N,N-bis(2-chloroethyl)-N-nitrosourea (BCNU) to decrease tissue glutathione reductase activity. We then exposed these animals and their matched vehicle-treated controls to 100% O2 at 4 ATA. Animals that received BCNU and were immediately exposed to hyperbaric O2 showed enhanced toxicity by seizing earlier in the exposure than controls. Animals that received BCNU 18 h before the hyperbaric O2 exposure were paradoxically protected from the effects of the exposure with a prolongation of their time to initial seizure and a marked increase in their survival time during the exposure. Tissue glutathione concentrations were also measured in the various groups and the hyperbaric O2 exposure produced marked decreases in hepatic glutathione levels in all control animals. In animals treated with BCNU 18 h before exposure, hepatic glutathione concentrations also decreased, but the concentrations had significantly increased during the 18-h waiting period, allowing these animals to maintain hepatic levels in the normal range even during their hyperbaric exposures. We conclude that treatment of rats with BCNU 18 h before exposure to hyperbaric hyperoxia results in enhanced protection of the animals during the exposure.     

Species traits and channel architecture mediate flow disturbance impacts on invertebrate drift

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