Multi-scale Modeling of Animal Movement and General Behavior Data Using Hidden Markov Models with Hierarchical Structures

Hidden Markov models (HMMs) are commonly used to model animal movement data and infer aspects of animal behavior. An HMM assumes that each data point from a time series of observations stems from one of N possible states. The states are loosely connected to behavioral modes that manifest themselves at the temporal resolution at which observations are made. Due to advances in tag technology and tracking with digital video recordings, data can be collected at increasingly fine temporal resolutions. Yet, inferences at time scales cruder than those at which data are collected and, which correspond to larger-scale behavioral processes, are not yet answered via HMMs. We include additional hierarchical structures to the basic HMM framework, incorporating multiple Markov chains at various time scales. The hierarchically structured HMMs allow for behavioral inferences at multiple time scales and can also serve as a means to avoid coarsening data. Our proposed framework is one of the first that models animal behavior simultaneously at multiple time scales, opening new possibilities in the area of animal movement and behavior modeling. We illustrate the application of hierarchically structured HMMs in two real-data examples: (i) vertical movements of harbor porpoises observed in the field, and (ii) garter snake movement data collected as part of an experimental design. Supplementary materials accompanying this paper appear online.     

Rice Germin-Like Proteins: Allelic Diversity and Relationships to Early Stress Responses

Germin-like protein (GLP) markers were associated with quantitative trait loci (QTL) for resistance to the rice blast pathogen, Magnaporthe oryzae in multiple rice (Oryza sativa) mapping populations. Twelve paralogous OsGLP gene family members are located within the physical QTL region on chromosome 8, and gene silencing studies suggest that they contribute collectively to the resistance phenotype. We compared sequence and expression profiles of OsGLP alleles in two resistant and two susceptible parental rice lines to find functional polymorphisms that correlated with the resistant phenotype. Based on coding and promoter sequences, the genes belong to two germin subfamily groups (GER3 and GER4). OsGLP members from both subfamilies were constitutively expressed and developmentally regulated in all cultivars. Transient induction above constitutive levels was observed for some OsGLPs, especially GER4 subfamily members, at early time points after M. oryzae infection and mechanical wounding. Varying 5′ regulatory regions and differential expression of some family members between resistant and susceptible cultivars corresponded with differential hydrogen peroxide (H₂O₂) accumulation after the same stimuli. OsGLP of both GER subfamilies localized to the plant cell wall. The protein location and early gene induction suggest that OsGLPs protect rice leaves at early stages of infection before fungal penetration and subsequent ingress. Our data suggest that regulation of OsGLP genes defines resistant versus susceptible phenotypes.     

Productivity of temperate broad-leaved forest stands differing in tree species diversity

? Understanding the effects of tree species diversity on biomass and production of forests is fundamental for carbon sequestration strategies, particularly in the perspective of the current climate change. However, the diversity-productivity relationship in old-growth forests is not well understood.

? We quantified biomass and above-ground production in nine forest stands with increasing tree species diversity from monocultures of beech to stands consisting of up to five deciduous tree species (Fagus sylvatica, Fraxinus excelsior, Tilia spp., Carpinus betulus, Acer spp.) to examine (a) if mixed stands are more productive than monospecific stands, (b) how tree species differ in the productivity of stem wood, leaves and fruits, and (c) if beech productivity increases with tree diversity due to lower intraspecific competition and complementary resource use.

? Total above-ground biomass and wood production decreased with increasing tree species diversity. In Fagus and Fraxinus, the basal area-related wood productivity exceeded those of the co-occurring tree species, while Tilia had the highest leaf productivity. Fagus trees showed no elevated production per basal area in the mixed stands.

? We found no evidence of complementary resource use associated with biomass production. We conclude that above-ground productivity of old-growth temperate deciduous forests depend more on tree species-specific traits than on tree diversity itself.

     

Effect of the Medium Replacement Interval on the Viability,Growth and In Vitro Maturation of Isolated Caprine and Ovine Pre‐Antral Follicles

The aim of the present study was to evaluate the effects of different medium replacement intervals on the viability, antral cavity formation, growth and in vitro maturation (IVM) of oocytes from caprine and ovine pre‐antral follicles. Pre‐antral ovarian follicles (≥150 μm) were isolated from the ovarian cortex of goats and sheep and were individually cultured for 24 days using two different medium replacement intervals [2 days (T₁) or 6 days (T₂)]. Follicle development was evaluated on the basis of antral cavity formation, increases in follicular diameter and the presence of healthy cumulus oocyte complexes and fully grown oocytes. For caprine species, results showed a higher percentage (p < 0.05) of viable follicles in T₁ than T₂ from day 6 until the end of the culture. In addition, when comparing both treatments after the same culture duration, the rate of antrum formation was significantly higher in T₁ than in T₂ from day 12 onwards. Yet, in ovines, when both treatments were compared on day 24 of the culture, there were more viable follicles in T₂ than in T₁ (p < 0.05). In the caprine species, percentages of fully grown oocytes (≥110 μm) acceptable for IVM after 24 days of culture were significantly higher in normal follicles cultured in T₁ (30.0%) than in T₂ (6.7%; p < 0.05). On the other hand, in ovines, at the end of the culture, the percentage of oocytes destined for IVM was higher in T₂ than in T₁ (23.5% vs 2.9%; p < 0.05). In conclusion, under the same conditions, the frequency of medium replacement significantly affected the in vitro development of caprine and ovine pre‐antral follicles. To improve the efficiency of the culture system, the medium must be replaced every 2 and 6 days for goat and sheep pre‐antral follicles, respectively.     

Validating the assessment of bull sperm morphology by veterinary practitioners

The objective of this study was to validate the assessment of bull sperm morphology done by veterinary practitioners. Out of 1606 bulls, 1400 (87.2%) and 1344 (83.7%) were designated by practitioners and an experienced andrologist, respectively, as having > 70% morphologically normal sperm. In 92% of the evaluations, there was agreement between the designations chosen.     

Modeling soil metabolic processes using isotopologue pairs of position-specific C-labeled glucose and pyruvate

Most organic carbon (C) in soils eventually turns into CO₂ after passing through microbial metabolic pathways, while providing cells with energy and biosynthetic precursors. Therefore, detailed insight into these metabolic processes may help elucidate mechanisms of soil C cycling processes. Here, we describe a modeling approach to quantify the C flux through metabolic pathways by adding 1-¹³C and 2,3-¹³C pyruvate and 1-¹³C and U-¹³C glucose as metabolic tracers to intact soil microbial communities. The model calculates, assuming steady-state conditions and glucose as the only substrate, the reaction rates through glycolysis, Krebs cycle, pentose phosphate pathway, anaplerotic activity through pyruvate carboxylase, and various biosynthesis reactions. The model assumes a known and constant microbial proportional precursor demand, estimated from literature data. The model is parameterized with experimentally determined ratios of ¹³CO₂ production from pyruvate and glucose isotopologue pairs. Model sensitivity analysis shows that metabolic flux patterns are especially responsive to changes in experimentally determined ¹³CO₂ ratios from pyruvate and glucose. Calculated fluxes are far less sensitive to assumptions concerning microbial chemical and community composition. The calculated metabolic flux pattern for a young volcanic soil indicates significant pentose phosphate pathway activity in excess of pentose precursor demand and significant anaplerotic activity. These C flux patterns can be used to calculate C use efficiency, energy production and consumption for growth and maintenance purposes, substrate consumption, nitrogen demand, oxygen consumption, and microbial C isotope composition. The metabolic labeling and modeling methods may improve our ability to study the biochemistry and ecophysiology of intact and undisturbed soil microbial communities.     

Technological Advances to Address Current Issues in Entomology: 2020 Student Debates

The 2020 Student Debates of the Entomological Society of America (ESA) were live-streamed during the Virtual Annual Meeting to debate current, prominent entomological issues of interest to members. The Student Debates Subcommittee of the National ESA Student Affairs Committee coordinated the student efforts throughout the year and hosted the live event. This year, four unbiased introductory speakers provided background for each debate topic while four multi-university teams were each assigned a debate topic under the theme ‘Technological Advances to Address Current Issues in Entomology’. The two debate topics selected were as follows: 1) What is the best taxonomic approach to identify and classify insects? and 2) What is the best current technology to address the locust swarms worldwide? Unbiased introduction speakers and debate teams began preparing approximately six months before the live event. During the live event, teams shared their critical thinking and practiced communication skills by defending their positions on either taxonomical identification and classification of insects or managing the damaging outbreaks of locusts in crops.     

Degradation of DEHP,PAHs and LAS in Source Separated MSW and Sewage Sludge During Composting

The efficiency of composting to remove the pollutants DEHP, PAHs and LAS from organic waste products was investigated. Source separated MSW and sewage sludge, respectively, were composted at temperatures ranging from 35 to 70°C using a laboratory-scale reactor composting system. At regular intervals, compost samples were taken from the reactors for chemical analysis. DEHP disappeared rapidly during composting of MSW; 96 to 99% of the initial content was degraded within 25 days of composting regardless of process temperature. In sewage sludge, the highest degradation of 91% was reached at a composting temperature of 65°C. LAS degradation in sewage sludge was fastest at 55°C, but at both process temperatures tested 99% of the initial content had been removed within 25 days. Degradation of PAHs was less complete. However, in all composting experiments, with MSW as well as sewage sludge, the final PAH concentration was less than in the starting material. Further experiments suggested that less than 0.1% of the pollutants had evaporated. Thus, composting proved to be a promising technique to promote degradation of organic pollutants — especially DEHP and LAS — in MSW and sewage sludge.