Information Sets and Excess Zeros in Random Effects Modeling of Longitudinal Data

Marginal regression via generalized estimating equations is widely used in biostatistics to model longitudinal data from subjects whose outcomes and covariates are observed at several time points. In this paper we consider two issues that have been raised in the literature concerning the marginal regression approach. The first is that even though the past history may be predictive of outcome, the marginal approach does not use this history. Although marginal regression has the flexibility of allowing between-subject variations in the observation times, it may lose substantial prediction power in comparison with the transitional modeling approach that relates the responses to the covariate and outcome histories. We address this issue by using the concept of “information sets” for prediction to generalize the “partly conditional mean” approach of Pepe and Couper (J. Am. Stat. Assoc. 92:991–998, 1997). This modeling approach strikes a balance between the flexibility of the marginal approach and the predictive power of transitional modeling. Another issue is the problem of excess zeros in the outcomes over what the underlying model for marginal regression implies. We show how our predictive modeling approach based on information sets can be readily modified to handle the excess zeros in the longitudinal time series. By synthesizing the marginal, transitional, and mixed effects modeling approaches in a predictive framework, we also discuss how their respective advantages can be retained while their limitations can be circumvented for modeling longitudinal data.     

Substrate and Target Sequence Length Influence RecTEPsy Recombineering Efficiency in Pseudomonas syringae

We are developing a new recombineering system to assist experimental manipulation of the Pseudomonas syringae genome. P. syringae is a globally dispersed plant pathogen and an important model species used to study the molecular biology of bacteria-plant interactions. We previously identified orthologs of the lambda Red bet/exo and Rac recET genes in P. syringae and confirmed that they function in recombineering using ssDNA and dsDNA substrates. Here we investigate the properties of dsDNA substrates more closely to determine how they influence recombineering efficiency. We find that the length of flanking homologies and length of the sequences being inserted or deleted have a large effect on RecTE_Psy mediated recombination efficiency. These results provide information about the design elements that should be considered when using recombineering.     

Physiological state influences the antennal response of Anastrepha obliqua to male and host volatiles

The sexual and host‐related behaviours of the fruit fly Anastrepha obliqua Macquart (Diptera: Tephritidae) are mediated by volatile compounds. However, whether the physiological state of this species affects its antennal and behavioural responses to semiochemicals is unknown. The effects of age, mating status, diet and the topical application of methoprene, a Juvenile hormone analogue (JHA), on the antennal sensitivity of this tephritid fruit fly species to selected male [(Z)‐3‐nonenol] and host fruit volatiles (ethyl benzoate, ethyl hexanoate, ethyl butyrate and trans‐β‐ocimene) are investigated using electroantennography (EAG). Overall, (Z)‐3‐nonenol and ethyl benzoate elicit the highest EAG responses in both sexes. Flies of both sexes aged 1, 5 and 10 days old show higher EAG responses to the tested compounds compared with flies aged 20 days old. Virgin females and males show higher EAG responses to volatile compounds than mated flies. Females and males fed with sugar plus protein show higher antennal responses to volatiles compared with flies fed sugar or protein alone. Flies of both sexes treated with methoprene show higher antennal responses than flies treated with acetone (control). These results suggest that the peripheral olfactory system in A. obliqua is modulated by the physiological state of the flies.     

Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil

Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop.     

MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria

MamA is a highly conserved protein found in magnetotactic bacteria (MTB), a diverse group of prokaryotes capable of navigating according to magnetic fields – an ability known as magnetotaxis. Questions surround the acquisition of this magnetic navigation ability; namely, whether it arose through horizontal or vertical gene transfer. Though its exact function is unknown, MamA surrounds the magnetosome, the magnetic organelle embedding a biomineralised nanoparticle and responsible for magnetotaxis. Several structures for MamA from a variety of species have been determined and show a high degree of structural similarity. By determining the structure of MamA from Desulfovibrio magneticus RS-1 using X-ray crystallography, we have opened up the structure-sequence landscape. As such, this allows us to perform structural- and phylogenetic-based analyses using a variety of previously determined MamA from a diverse range of MTB species across various phylogenetic groups. We found that MamA has remained remarkably constant throughout evolution with minimal change between different taxa despite sequence variations. These findings, coupled with the generation of phylogenetic trees using both amino acid sequences and 16S rRNA, indicate that magnetotaxis likely did not spread via horizontal gene transfer and instead has a significantly earlier, primordial origin.     

Informing conservation by identifying range shift patterns across breeding habitats and migration strategies

A species distribution combines the resources and climatic tolerances that allow an individual or population to persist. As these conditions change, one mechanism to maintain favorable resources is for an organism to shift its range. Much of the research examining range shifts has focused on dynamic distribution boundaries wheras the role of species breeding habitat or migration strategies on shift tendencies has received less attention. We expand on previous research by using a large suite of avian species (i.e., 277), analyzing observed abundance-weighted average latitudes, and categorizing species by breeding environment and migration strategy. We used the North American Breeding Bird Survey dataset to address two questions: (1) Has the center of observed abundance for individual species shifted latitudinally? (2) Is there a relationship between migration strategy or breeding habitat and range shifts? Results indicate the majority of species have experienced poleward range shifts over the last 43 years, and birds breeding in all habitat showed trends of poleward shift but only those species breeding in scrub-shrub and grassland environments were different from zero. Additionally, species that are short distance migrants are experiencing significant poleward shifts while Neotropical and permanent residents had shifts that were not different from zero. Our findings do support the general trend expected from climate driven changes (i.e., > 52 % shifting poleward), however, the proportion of species exhibiting equatorial shifts (24 %) or no significant shifts (23 %) illustrates the complex interplay between land cover, climate, species interactions, and other forces that can interact to influence breeding ranges over time. Regardless of the mechanisms driving range shifts, our findings emphasize the need for connecting and expanding habitats for those species experiencing range shifts. This research describes the patterns of breeding birds through central North America and we encourage future research to focus on the mechanisms driving these patterns.