Biology subjects

Miller, N. J.

Publications and source records attributed to Miller, N. J..

8 recordsLinked to original sources

bioRxiv2025

Insect Identification with ESEM Imaging and DNA Barcoding for Forensic Use

Flies are among the first insects to arrive at a corpse to lay eggs. The developing larvae can be used to determine post-mortem interval (PMI) using species specific growth models. The larvae can be difficult to identify due to minute morphological characteristics and rearing larvae into adults is time consuming and may be unsuccessful. We investigated the potential of coupling Environmental Scanning Electron Microscopy (ESEM) and DNA barcoding to enable the acquisition of high resolution images while obtaining DNA in a minimally destructive manner. This study focused on the widespread and forensically relevant species Chrysomya rufifacies as a model. Specimens were prepared in three different drying treatments: unaltered, dried, dried and imaged. Following the imaging process, three different DNA extraction methods with different levels of sample destruction were tested. ESEM imaging showed that there were no visual differences between specimens that underwent drying treatments and ones that were not dried. No significant differences in DNA yield were observed for drying treatments and extraction methods post extraction. However, extraction methods demonstrated significant differences in yield of PCR products. Sequenced PCR products aligned with 100% identity to the C. rufifacies mitochondrial genome reference sequence. Lower nucleotide identities between the sequenced PCR products and other forensically relevant fly species demonstrated that combining ESEM and DNA barcoding is a promising approach to rapid and reliable identification of insect larvae recovered from forensic samples.

genetics↗

bioRxiv2023

A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/sec) and low closed-loop latencies (<1ms) that uses a novel 0.3 mm thin tether to minimize behavioral impact. Head position and rotation are tracked in 3D and used to drive active commutation without torque measurements. ONIX can acquire from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, 3D-trackers, and other data sources. We used ONIX to perform uninterrupted, long ([~]7 hours) neural recordings in mice as they traversed complex 3-dimensional terrain. ONIX allowed exploration with similar mobility as non-implanted animals, in contrast to conventional tethered systems which restricted movement. By combining long recordings with full mobility, our technology will enable new progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

neuroscience↗

bioRxiv2022

Natural occurrence and analysis of Nosema sp. infection in the adult population of western bean cutworm in Michigan

An understanding of population dynamics and insect biology is important for effective crop management strategies. Biotic factors such as pathogens play a large role on the fitness and dynamics of insect populations. Microsporidia are obligate intracellular parasites that infect more than 150 insect species and range from sublethal and chronic to fast acting and deadly. The western bean cutworm, Striacosta albicosta (Smith) (Lepidoptera: Noctuidae), is a pest of both corn (Zea maize L.) and dry beans (Phaseolus sp L.) that is infected by a microsporidian parasite from the genus Nosema. Unfortunately, little is known about the interactions between the Nosema sp. infecting the western bean cutworm and its prevalence and effects on the host population. This is especially true for the western bean cutworm population that has settled in the Great Lakes region over the last two decades. Using field caught samples and phase contrast microscopy, we found a 100% prevalence of infection in the adult western bean cutworm population in Michigan. No consistent trends in pathogen load were observed over the course of the western bean cutworm flight season. A weak, but statistically significant relationship was observed between male body weight and pathogen load.

ecology↗

bioRxiv2022

Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex

From visual perception to language, sensory stimuli change their meaning depending on prior experience. Recurrent neural dynamics can interpret stimuli based on externally cued context, but it is unknown whether similar dynamics can compute and employ internal hypotheses to resolve ambiguities. Here, we show that mouse retrosplenial cortex (RSC) can form hypotheses over time and perform spatial reasoning through recurrent dynamics. In our task, mice navigated using ambiguous landmarks that are identified through their mutual spatial relationship, requiring sequential refinement of hypotheses. Neurons in RSC and in artificial neural networks encoded mixtures of hypotheses, location, and sensory information, and were constrained by robust low dimensional dynamics. RSC encoded hypotheses as locations in activity space with divergent trajectories for identical sensory inputs, enabling their correct interpretation. Our results indicate that interactions between internal hypotheses and external sensory data in recurrent circuits can provide a substrate for complex sequential cognitive reasoning.

neuroscience↗

bioRxiv2021

Genome size evolution in the beetle genus Diabrotica

Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 - 1.64 gigabase pairs (Gb) and between 2.26-2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of fucata group and virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements (MITEs) and gypsy-like long terminal repeat (LTR) retroelements.

genomics↗

bioRxiv2020

Contribution of different host plants to the adult population of western bean cutworm

The western bean cutworm, Striacosta albicosta (Smith) (Lepidoptera: Noctuidae), is historically a pest of both corn (Zea mays L.) and dry beans (Phaseolus sp L.) in the western Great Plains. However, it has recently undergone an eastward range expansion establishing itself across the Corn Belt in twenty-five states and four Canadian provinces. To mitigate the effects of infestation in Michigan, foliar insecticides are used in dry beans whereas management of the pest in corn relies more heavily on the use of Bt-expressing hybrids. In this study stable carbon isotope analysis was used to determine what crop adult moths developed on as larvae with analysis showing that very few of the adult moths developed on dry beans. These results suggest that beans and corn are not suitable as co-refuges and that mainly adults which developed on corn are contributing to the next generation of western bean cutworm in Michigan.

ecology↗

bioRxiv2017

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

genomics↗

bioRxiv2017

Colonization History Of The Western Corn Rootworm (Diabrotica virgifera virgifera) In North America: Insights From Random Forest ABC Using Microsatellite Data

First described from western Kansas, USA, the western corn rootworm, Diabrotica virgifera virgifera, is one of the worst pests of maize. The species is generally thought to be of Mexican origin and to have incidentally followed the expansion of maize cultivation into North America thousands of years ago. However, this hypothesis has never been investigated formally. In this study, the genetic variability of samples collected throughout North America was analysed at 13 microsatellite marker loci to explore precisely the population genetic structure and colonization history of D. v. virgifera. In particular, we used up-to-date Approximate Bayesian Computation methods based on random forest algorithms to test a Mexican versus a central-USA origin of the species, and to compare various possible timings of colonization. This analysis provided strong evidence that the origin of D. v. virgifera was southern (Mexico, or even further south). Surprisingly, we also found that the expansion of the species north of its origin was recent - probably not before 1100 years ago - thus indicating it was not directly associated with the early history of maize expansion out of Mexico, a far more ancient event.

evolutionary biology↗