Mark-recapture statistics and demographic analysis

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2002Mark-recapture analysis of populations is becoming an important tool in population biology. Mark-recapture methods can be used to estimate transition probabilities among life-stages from capture histories of marked individuals for which stages can be determined at each sampling occasion. This method is called a multi-stage mark-recapture (MSMR) method. In this thesis, I describe advances I made in the MSMR method and present analyses that apply this method to actual data. The advances I made in the MSMR method are motivated by a need to provide a link between mark-recapture data and demographic models such as matrix population models and integrodifference models. I resolve some issues that are commonly encountered during sampling, such as the fact that the sex or life-stage of some individuals is unknown during some sampling occasions and that individuals become unobservable during some life-stages. I introduce a stage-structure that permits simple conversion of estimated transition probabilities into a matrix population model. I describe an algorithm to simplify programming for parameter estimation. I also introduce a method to estimate the distribution of dispersal displacements (a dispersal kernel) from mark-recapture data. I apply some of the methods described above to data of the North Atlantic right whale (Eubalaena glacialis) The right whales are considered one of the most endangered mammals. The current population size is about 300 in the northwestern Atlantic, and the number is declining. I applied the multi-stage mark-recapture statistics to the 17-year individual sighting history data. Using the estimated transition probabilities, I constructed a population projection matrix, which was used for further demographic analyses. I found that the population was slowly increasing in 1980, but it started to decline slowly around 1992. I show that (1) this change was caused by increased mortality of females that have just given birth, (2) protecting two females a year from the deaths is enough to prevent the declining trend, and (3) demographic stochasticity is a more important factor influencing their long-term viability than environmental stochasticity.The David and Lucile Packard Foundation, the Rinehart Coastal Research Center, and the Woods Hole Oceanographic Institution Sea Grant Program (NOAA NA86RG0075) supported this work through grants to Hal Caswell. Graduate Research Fellowship from Woods Hole Oceanographic Institution also supported the first year of my study

IDENTIFYING INTERACTIONS AMONG SALMON POPULATIONS FROM OBSERVED DYNAMICS

Abstract. A simple direct correlation analysis of individual counts between different populations often fails to characterize the true nature of population interactions; however, the most common data type available for population studies is count data, and one of the most important objectives in population and community ecology is to identify interactions among populations. Here, I examine the dynamics of the spawning abundance of fall-run chinook salmon spawning within the California Central Valley and the Klamath Basin, California, and the Columbia River Basin, Oregon. I analyzed multiple time series from each watershed using a multivariate time-series technique called maximum autocorrelation factor analysis. This technique was used for finding common underlying trends in escapement abundance within each watershed. These trends were further investigated to identify potential resource-mediated interactions among the three groups of salmon. Each group is affected by multiple trends that are likely to be affected by environmental factors. In addition, some of the trends are coherent with each other, and the differences in population dynamics originate from variations in the relative importance of these trends among the three watershed groups

The Effects of Disease-Induced Juvenile Mortality on the Transient and Asymptotic Population Dynamics of Chinook Salmon (Oncorhynchus tshawytscha)

The effects of an increased disease mortality rate on the transient and asymptotic dynamics of Chinook salmon (Oncorhynchus tshawytscha) were investigated. Disease-induced mortality of juvenile salmon has become a serious concern in recent years. However, the overall effects of disease mortality on the asymptotic and transient dynamics of adult spawning abundance are still largely unknown. We explored various scenarios with regard to the density-dependent process, the distribution of survivorship over the juvenile phase, the disease mortality rate, and the infusion of stray hatchery fish. Our results suggest that the sensitivity to the disease mortality rate of the equilibrium adult spawning abundance and resilience (asymptotic return rate toward this equilibrium following a small perturbation) varied widely and differently depending on the scenario. The resilience and coefficient of variation of adult spawning abundance following a large perturbation were consistent with each other under the scenarios investigated. We conclude that the increase in disease mortality likely has an effect on fishery yield under a fluctuating environment, not only because the mean equilibrium adult spawning abundance has likely been reduced, but also because the resilience has likely decreased and the variance in adult spawning abundance has likely increased. We also infer the importance of incorporating finer-scale spatiotemporal information into population models and demonstrate a means for doing so within a matrix population modeling framework.The open access fee for this work was funded through the Texas A&M University Open Access to Knowledge (OAK) Fund

A critical analysis of the pneumatology of Thomas Erskine of Linlathen

In performing an analysis of the pneumatology of Thomas Erskine it is first necessary to look for the presence of a traditional Trinitarian Pneumatology which is based on the historical findings of the church and which deals with the subject of hypostasis and the relationships between the Persons within the Godhead. This kind of pneumatology is found to be lacking in Erskine’s writings. The next step is to proceed to look for anything that could replace it. Erskine’s concept of the “first bond” of the flesh, the role of the human conscience, and the place of the living Word are three things that partially take the place of a formal pneumatology in Erskine’s thinking. Erskine was very interested in the West Country revival which began in Scotland in 1829. He visited the area and wrote about his observations and experiences there. This increased his interest in the actions of the Holy Spirit both in experience and the scriptures. Even though he later recanted his endorsement of these manifestations in his own day, he held to his belief that such phenomena should appear in a healthy church which follows a New Testament pattern. In this thesis Erskine’s writings are analyzed by scanning all of them into a computer database and searching for references to the actions of the Holy Spirit. From this a dynamic pneumatology emerges. A dynamic pneumatology is not concerned with historic creeds or the relationships within the Godhead, John McIntyre defines a dynamic pneumatology as one that speaks of what the Holy Spirit does. McIntyre’s taxonomy sets forth eleven patterns of dynamic pneumatology with many sub-patterns. This examination of the writings of Erskine reveals a strong dynamic pneumatology which is both relational and ecclesial

MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus

ヒト細胞内でRNA分解時に働く因子の役割を解明 --細胞内におけるRNA分解機構の全容解明に期待--. 京都大学プレスリリース. 2022-08-05.Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here, we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent substrate decay by the human exosome. Using RNA polymerase II-transcribed poly(A)⁺ substrate accumulation as an indicator of a perturbed exosome, we found functional redundancy between RRP6 and MPP6 in the decay of these poly(A)⁺ transcripts. MTR4 binding to the exosome core via MPP6 was essential for MPP6 to exert its redundancy with RRP6. However, at least for the decay of our identified exosome substrates, MTR4 recruitment by MPP6 was not functionally equivalent to recruitment by RRP6. Genome-wide classification of substrates based on their sensitivity to each exosome component revealed that MPP6 deals with a specific range of substrates and highlights the importance of MTR4 for their decay. Considering recent findings of competitive binding to the exosome between auxiliary complexes, our results suggest that the MPP6-incorporated MTR4-exosome complex is one of the multiple alternative complexes rather than the prevailing one

Significance of IgG4-positive cells in severe eosinophilic chronic rhinosinusitis

Background: IgG4 production is regulated by type 2 (IL-4 and IL-13) and regulatory (IL-10) cytokines involved in the pathophysiology of chronic rhinosinusitis (CRS). We sought to determine the pathophysiological characteristics of IgG4-positive cells in sinonasal tissues in CRS, especially eosinophilic CRS (ECRS). Methods: IgG4-positive cells in uncinate tissues (UT) and nasal polyps (NP) were examined by immunohistochemistry. Associations between the number of IgG4-positive cells and clinicopathological factors were analyzed. Receiver operating characteristics (ROC) analysis was performed to determine the cut-off value of IgG4-positive cells in tissue that can predict the post-operative course. Results: IgG4 was mainly expressed in infiltrating plasma and plasmacytoid cells, and the number of IgG4-positive cells was significantly higher in NP, especially those from severe ECRS patients, than in UT. In CRS patients, the number of IgG4-positive cells significantly and positively correlated with blood and tissue eosinophilia, radiological severity, and serum level of total IgE. The number of infiltrating IgG4-positive cells was significantly higher in patients with a poor post-operative course (sustained sinus shadow 6 months after surgery) than in those with a good one. The number of IgG4-positive cells in NP could discriminate patients with a good or a poor post-operative course (area under the curve: 0.769). Also, 73.3% sensitivity and 82.5% specificity were achieved when the cut-off value was set at 17 cells/high-power field. Conclusions: Our results suggest that the local expression of IgG4 on cells may be used as a biomarker that reflects the pathophysiology of CRS, including the post-operative course