Bovine Viral Diarrhea Virus-1 () Associated with Stillborn and Mummified Fetuses in Farmed White-Tailed Deer () in Florida.

Bovine viral diarrhea virus (BVDV) is a globally significant pathogen affecting both domestic livestock and wildlife, including white-tailed deer (WTD; ). While experimental infections have demonstrated WTD susceptibility to BVDV, natural infections and associated reproductive outcomes remain scarcely documented. Here, we report the first confirmed case of naturally occurring BVDV-1 infection associated with fetal mummification in farmed WTD in Florida.

A realistic phantom dataset for benchmarking cryo-ET data annotation.

Cryo-electron tomography (cryo-ET) is a powerful technique for imaging molecular complexes in their native cellular environments. However, identifying the vast majority of molecular species in cellular tomograms remains prohibitively difficult. Machine learning (ML) methods provide an opportunity to automate the annotation process, but algorithm development has been hindered by the lack of large, standardized datasets.

Fascioloides magna infection in a captive impala (Aepyceros melampus) in Florida, USA.

Parasitic diseases are associated with diverse clinical signs, and veterinary professionals must be familiar with the presentations of infections in a variety of hosts. As human activity introduces new and exotic host species, expanding our understanding of pathogen effects in new species becomes integral to effective surveillance, diagnosis, and treatment. This article presents the expansion of the known host range of the American liver fluke, Fascioloides magna, with the infection of a farmed impala (Aepyceros melampus) in Marion County, Florida, USA.

Gross pathology and epidemiological features of mule deerpox virus infections in farmed white-tailed deer (Odocoileus virginianus) in Florida.

Mule deerpox virus (DPV) is a member of the Poxviridae family that affects various deer species, causing crustaceous skin lesions and potentially lethal infections. In this study, we aimed to investigate the spatial and temporal distribution of DPV in farmed white-tailed deer (WTD; Odocoileus virginianus) in Florida, USA, from 2017 to 2023. Necropsies were performed, and specimens were collected from 776 deer.

Infection in a Farmed White-Tailed Deer () in Florida, USA.

A 7-year-old farmed white-tailed deer doe was transported to a Levy County, Florida property and began to decline in health, exhibiting weight loss and pelvic limb weakness. The doe prematurely delivered live twin fawns, both of which later died. The doe was treated with corticosteroids, antibiotics, gastric cytoprotectants, and B vitamins but showed no improvement.

Recent advances in data collection for Cryo-EM methods.

Methods of transmission electron microscopy (TEM) are typically used to resolve structures of vitrified biological specimens using both single particle analysis (SPA) and tomographic methods and use both conventional as well as scanning transmission modes of data collection. Automation of data collection for each method has been developed to different levels of convenience for the users. Automation of methods using the conventional TEM mode has progressed the furthest.

A novel bluetongue virus serotype 2 strain isolated from a farmed Florida white-tailed deer (Odocoileus virginianus) arose from reassortment of gene segments derived from co-circulating serotypes in the Southeastern USA.

Bluetongue disease is a reportable animal disease that affects wild and farmed ruminants, including white-tailed deer (WTD). This report documents the clinical findings, ancillary diagnostics, and genomic characterization of a novel reassortant bluetongue virus serotype 2 (BTV-2) strain isolated from a dead Florida farmed WTD in 2022. Our analyses support that this BTV-2 strain likely stemmed from the acquisition of genome segments from co-circulating BTV strains in Florida and Louisiana.

Learning to automate cryo-electron microscopy data collection with Ptolemy.

Over the past decade, cryo-electron microscopy (cryoEM) has emerged as an important method for determining near-native, near-atomic resolution 3D structures of biological macromolecules. To meet the increasing demand for cryoEM, automated methods that improve throughput and efficiency of microscope operation are needed. Currently, the targeting algorithms provided by most data-collection software require time-consuming manual tuning of parameters for each grid, and, in some cases, operators must select targets completely manually.

Fully automated multi-grid cryoEM screening using Smart Leginon.

Single-particle cryo-electron microscopy (cryoEM) is a swiftly growing method for understanding protein structure. With increasing demand for high-throughput, high-resolution cryoEM services comes greater demand for rapid and automated cryoEM grid and sample screening. During screening, optimal grids and sample conditions are identified for subsequent high-resolution data collection.

Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy.

Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.

Small Molecule Microcrystal Electron Diffraction for the Pharmaceutical Industry-Lessons Learned From Examining Over Fifty Samples.

The emerging field of microcrystal electron diffraction (MicroED) is of great interest to industrial researchers working in the drug discovery and drug development space. The promise of being able to routinely solve high-resolution crystal structures without the need to grow large crystals is very appealing. Despite MicroED's exciting potential, adoption across the pharmaceutical industry has been slow, primarily owing to a lack of access to specialized equipment and expertise.

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels.

Thermal homeostasis of mammals is constrained by body-size scaling. Consequently, small mammals require considerable energy to maintain a high mass-specific metabolic rate (MSMR) and sustain target body temperature. In association with gut microbiota, mammalian hosts acquire absorbable molecules and fulfill their metabolic requirements.

Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem.

Gut microbial communities of animals are influenced by diet and seasonal weather changes. Since foraging strategies of wild animals are affected by phenological changes, gut microbial communities would differ among seasons. However, interactions of plant-animal-microbiota with seasonal changes have not been well characterized.

High resolution single particle cryo-electron microscopy using beam-image shift.

Automated data acquisition is used widely for single-particle reconstruction of three-dimensional (3D) volumes of biological complexes preserved in vitreous ice and imaged in a transmission electron microscope. Automation has become integral to this method because of the very large number of particle images required in order to overcome the typically low signal-to-noise ratio of these images. For optimal efficiency, automated data acquisition software packages typically employ some beam-image shift targeting as this method is both fast and accurate (±0.

Routine determination of ice thickness for cryo-EM grids.

Recent advances in instrumentation and automation have made cryo-EM a popular method for producing near-atomic resolution structures of a variety of proteins and complexes. Sample preparation is still a limiting factor in collecting high quality data. Thickness of the vitreous ice in which the particles are embedded is one of the many variables that need to be optimized for collection of the highest quality data.

Benchmarking cryo-EM Single Particle Analysis Workflow.

Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis.

Routine single particle CryoEM sample and grid characterization by tomography.

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface.

Best practices for managing large CryoEM facilities.

This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6-7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.

Automated data collection in single particle electron microscopy.

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described.

Multiplexed TEM Specimen Preparation and Analysis of Plasmonic Nanoparticles.

We describe a system for rapidly screening hundreds of nanoparticle samples using transmission electron microscopy (TEM). The system uses a liquid handling robot to place up to 96 individual samples onto a single standard TEM grid at separate locations. The grid is then transferred into the TEM and automated software is used to acquire multiscale images of each sample.

MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography.

The MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes the kind of data held, together with other important metadata. In response to advances in electron microscopy techniques, a number of variants to the file format have emerged which contain useful additional data, but which limit interoperability between different software packages.