The microbial fermentation of plant feed by ruminants produces enteric methane (CH4), a potent greenhouse gas. Supplementing ruminant diets with an experimental methane inhibitor, 3-nitrooxypropanol (3-NOP), has been shown to decrease enteric CH4 production, but the effect of manure from these cattle on the soil microbiome has not been studied. In 2017 and 2018, we examined the effects of stockpiled manure and composted manure from cattle fed 3-NOP supplement alone or in combination with monensin (an ionophore) on soil permanganate-oxidizable C, microbial biomass C (MBC), the composition and diversity of prokaryotic and fungal commu-nities, and the activities of beta-glucosidase (C cycling), N-acetyl-beta-glucosaminidase (C and N cycling), acid and alkaline phosphomonoesterases (P cycling), and arylsuphatase (S cycling) in a forage cropping system. Stock -piled or composted manure from cattle fed 3-NOP increased MBC in 2017, fungal alpha-diversity in 2018 and the relative abundance of Actinobacteriota, but it decreased the relative abundances of Acidobacteriota and Basidio-mycota, relative to stockpiled or composted manure from cattle that were not fed 3-NOP. In 2017, relative to the conventional stockpiled manure, 3-NOP in stockpiled manure increased the activities of N-acetyl-beta-glucosami-nidase and acid phosphomonoesterase, but these effects were not observed for composted manure. Monensin, when used in combination with 3-NOP, did not affect any of the soil parameters measured in this study. The core microbiome found in 90 % of the soil samples included the bacterial and fungal genera Vicinamibacteraceae and Solicoccozyma, respectively. Therefore, 3-NOP manure or compost altered the composition of the soil micro-biome, and the 3-NOP in stockpiled manure increased the potential activities of enzymes involved in C-and-N and P cycling in the first year of the study, and fungal alpha-diversity in the second year, but no negative or persistent effects of 3-NOP on enzyme activities were observed.

Potato tuber shape is an important quality trait for breeding and variety development. Length to width (L/W) ratio is a commonly used method to score potato tubers for suitability for different markets and is relatively easy to measure, though labor intensive when done manually. L/W also does not adequately capture secondary growth and other tuber malformations that contribute to tuber shape. Tuber shape has a genetic component and is a prime target for early breeding selection. In the current study we developed an image analysis pipeline to extract tuber shape statistics from images taken using inexpensive, commercially available cameras. The image processing pipeline was used to evaluate greenhouse grown tubers from 32 unique crosses. Tubers from greenhouse grown plants were then grown in a field located in Vauxhall, AB, Canada, and evaluated for tuber shape. Randomly selected tuber images were also shown to industry agronomists and potato growers located in Southern Alberta and their shape scored for suitability for processing (French fry and chipping) markets. Based on measurements taken from greenhouse grown tubers we were able to classify whether mean tuber shape from field grown plants were within ideal shape parameters for processing markets with ~76–86% accuracy. Based on performance of progeny we identified parents which show higher breeding value for tuber shape.

Transgenic immediate-early gene reporter mouse strains are valuable tools for studying activity-dependent neural cell populations in vivo. However, routine characterization of the Gene Expression Nervous System Atlas (GENSAT) "Egr1-EGFP" reporter mouse strain produced results that were highly inconsistent with endogenous Egr1 expression. Activity-dependent EGFP expression was not observed, and EGFP protein did not co-localize with native Egr1 protein. This precautionary study outlines the limitations of the Egr1-EGFP transgenic line as a tool to study the activity-dependent expression of Egr1 and emphasizes the necessity of taking into account the potential loss of regulatory elements, stability determinants, or translational modulation in transgenic reporter strains.

Immediate-early genes (IEGs) exhibit a rapid, transient transcription response to neuronal activation. Fluorescently labeled mRNA transcripts appear as bright intranuclear transcription foci (INF), which have been used as an all-or-nothing indicator of recent neuronal activity; however, it would be useful to know whether INF fluorescence can be used effectively to assess relative activations within a neural population. We quantified the Homer1a (H1a) response of hippocampal neurons to systematically varied numbers of exposures to the same places by inducing male Long-Evans rats to run laps around a track. Previous studies reveal relatively stable firing rates across laps on a familiar track. A strong linear trend (r2  > 0.9) in INF intensity was observed between 1 and 25 laps, after which INF intensity declined as a consequence of dispersion related to the greater elapsed time. When the integrated fluorescence of the entire nucleus was considered instead, the linear relationship extended to 50 laps. However, there was only an approximate doubling of H1a detected for this 50-fold variation in total spiking. Thus, the intranuclear H1a RNA fluorescent signal does provide a relative measure of how many times a set of neurons was activated over a ~10 min period, but the dynamic range and hence signal-to-noise ratios are poor. This low dynamic range may reflect previously reported reductions in the IEG response during repeated episodes of behavior over longer time scales. It remains to be determined how well the H1a signal reflects relative firing rates within a population of neurons in response to a single, discrete behavioral event.

Epileptic seizures represent altered neuronal network dynamics, but the temporal evolution and cellular substrates of the neuronal activity patterns associated with spontaneous seizures are not fully understood. We used simultaneous recordings from multiple neurons in the hippocampus and neocortex of rats with chronic temporal lobe epilepsy to demonstrate that subsets of cells discharge in a highly stereotypical sequential pattern during ictal events, and that these stereotypical patterns were reproducible across consecutive seizures. In contrast to the canonical view that principal cell discharges dominate ictal events, the ictal sequences were predominantly composed of fast-spiking, putative inhibitory neurons, which displayed unusually strong coupling to local field potential even before seizures. The temporal evolution of activity was characterized by unique dynamics where the most correlated neuronal pairs before seizure onset displayed the largest increases in correlation strength during the seizures. These results demonstrate the selective involvement of fast spiking interneurons in structured temporal sequences during spontaneous ictal events in hippocampal and neocortical circuits in experimental models of chronic temporal lobe epilepsy.

Background: Understanding the neurobiological basis of cognition and behavior, and disruptions to these processes following injury and disease, requires'a large-scale assessment of neural populations, and knowledge of their patterns of connectivity.New method: We present an analysis platform for large-scale investigation of functional and neuroanatomical connectivity in rodents. Retrograde tracers were injected and in a subset of animals behavioral tests to drive immediate-early gene expression were administered. This approach allows users to perform whole-brain assessment of function and connection in a semi-automated quantitative manner. Brains were cut in the coronal plane, and an image of the block face was acquired. Wide-field fluorescent scans of whole sections were acquired and analyzed using Matlab software.Results: The toolkit utilized open-source and custom platforms to accommodate a largely automated analysis pipeline in which neuronal boundaries are automatically segmented, the position of segmented neurons are co-registered with a corresponding image acquired during sectioning, and a 3-D representation of neural tracer (and other products) throughout the,entire brain is generated.Comparison with existing methods: Current whole brain connectivity measures primarily target mice and use anterograde tracers. Our focus on segmented units of interest (e.g., NeuN labeled neurons) and restricting measures to these units produces a flexible platform for a variety of whole brain analyses (measuring activation, connectivity, markers of disease, etc.).Conclusions: This open-source toolkit allows an investigator to visualize and quantify whole brain data in 3-D, and additionally provides a framework that can be rapidly integrated with user-specific analyses and methodologies. (C) 2016 Elsevier B.V. All rights reserved.

A central feature of theories of spatial navigation involves the representation of spatial relationships between objects in complex environments. The parietal cortex has long been linked to the processing of spatial visual information and recent evidence from single unit recording in rodents suggests a role for this region in encoding egocentric and world-centered frames. The rat parietal cortex can be subdivided into four distinct rostral-caudal and medial-lateral regions, which includes a zone previously characterized as secondary visual cortex. At present, very little is known regarding the relative connectivity of these parietal subdivisions. Thus, we set out to map the connectivity of the entire anterior-posterior and medial-lateral span of this region. To do this we used anterograde and retrograde tracers in conjunction with open source neuronal segmentation and tracer detection tools to generate whole brain connectivity maps of parietal inputs and outputs. Our present results show that inputs to the parietal cortex varied significantly along the medial-lateral, but not the rostral-caudal axis. Specifically, retrosplenial connectivity is greater medially, but connectivity with visual cortex, though generally sparse, is more significant laterally. Finally, based on connection density, the connectivity between parietal cortex and hippocampus is indirect and likely achieved largely via dysgranular retrosplenial cortex. Thus, similar to primates, the parietal cortex of rats exhibits a difference in connectivity along the medial-lateral axis, which may represent functionally distinct areas.