NIR Instruments and Prediction Methods for Rapid Access to Grain Protein Content in Multiple Cereals.

Achieving global goals for sustainable nutrition, health, and wellbeing will depend on delivering enhanced diets to humankind. This will require instantaneous access to information on food-source quality at key points of agri-food systems. Although laboratory analysis and benchtop NIR spectrometers are regularly used to quantify grain quality, these do not suit all end users, for example, stakeholders in decentralized agri-food chains that are typical in emerging economies. Therefore, we explored benchtop and portable NIR instruments, and the methods that might aid these particular end uses. For this purpose, we generated NIR spectra for 328 grain samples from multiple cereals (finger millet, foxtail millet, maize, pearl millet, and sorghum) with a standard benchtop NIR spectrometer (DS2500, FOSS) and a novel portable NIR-based instrument (HL-EVT5, Hone). We explored classical deterministic methods (via winISI, FOSS), novel machine learning (ML)-driven methods (via Hone Create, Hone), and a convolutional neural network (CNN)-based method for building the calibrations to predict grain protein out of the NIR spectra. All of the tested methods enabled us to build relevant calibrations out of both types of spectra (i.e., R2 ≥ 0.90, RMSE ≤ 0.91, RPD ≥ 3.08). Generally, the calibration methods integrating the ML techniques tended to enhance the prediction capacity of the model. We also documented that the prediction of grain protein content based on the NIR spectra generated using the novel portable instrument (HL-EVT5, Hone) was highly relevant for quantitative protein predictions (R2 = 0.91, RMSE = 0.97, RPD = 3.48). Thus, the presented findings lay the foundations for the expanded use of NIR spectroscopy in agricultural research, development, and trade.

3D Clearing and Molecular Labeling in Plant Tissues.

Plant histology and imaging traditionally involve the transformation of tissues into thin sections to minimize light scatter in opaque material, allowing optical clarity and high-resolution microscopy. Recently, new techniques in 3D tissue clearing, including PEA-CLARITY, have been developed to minimize light scatter within intact, whole samples. These techniques can achieve equivalent microscopic resolution to that of thin section imaging with the added benefit of maintaining the original 3D structure and position of biomolecules of interest. Furthermore, PEA-CLARITY is compatible with standard stains and immunohistochemistry, allowing molecular interrogation of intact, 3D tissues. This chapter outlines the current methods available for 3D histology in plants and details the materials, equipment, reagents, and procedure for the PEA-CLARITY technique.

Anatomical and Molecular Properties of Long Descending Propriospinal Neurons in Mice.

Long descending propriospinal neurons (LDPNs) are interneurons that form direct connections between cervical and lumbar spinal circuits. LDPNs are involved in interlimb coordination and are important mediators of functional recovery after spinal cord injury (SCI). Much of what we know about LDPNs comes from a range of species, however, the increased use of transgenic mouse lines to better define neuronal populations calls for a more complete characterisation of LDPNs in mice. In this study, we examined the cell body location, inhibitory neurotransmitter phenotype, developmental provenance, morphology and synaptic inputs of mouse LDPNs throughout the cervical and upper thoracic spinal cord. LDPNs were retrogradely labelled from the lumbar spinal cord to map cell body locations throughout the cervical and upper thoracic segments. Ipsilateral LDPNs were distributed throughout the dorsal, intermediate and ventral grey matter as well as the lateral spinal nucleus and lateral cervical nucleus. In contrast, contralateral LDPNs were more densely concentrated in the ventromedial grey matter. Retrograde labelling in GlyT2GFP and GAD67GFP mice showed the majority of inhibitory LDPNs project either ipsilaterally or adjacent to the midline. Additionally, we used several transgenic mouse lines to define the developmental provenance of LDPNs and found that V2b positive neurons form a subset of ipsilaterally projecting LDPNs. Finally, a population of Neurobiotin (NB) labelled LDPNs were assessed in detail to examine morphology and plot the spatial distribution of contacts from a variety of neurochemically distinct axon terminals. These results provide important baseline data in mice for future work on their role in locomotion and recovery from SCI.

Effects Of treadmill training on hindlimb muscles of spinal cord-injured mice.

INTRODUCTION: Treadmill training is known to prevent muscle atrophy after spinal cord injury (SCI), but the training duration required to optimize recovery has not been investigated. METHODS: Hemisected mice were randomized to 3, 6, or 9 weeks of training or no training. Muscle fiber type composition and fiber cross-sectional area (CSA) of medial gastrocnemius (MG), soleus (SOL), and tibialis anterior (TA) were assessed using ATPase histochemistry. RESULTS: Muscle fiber type composition of SCI animals did not change with training. However, 9 weeks of training increased the CSA of type IIB and IIX fibers in TA and MG muscles. CONCLUSIONS: Nine weeks of training after incomplete SCI was effective in preventing atrophy of fast-twitch muscles, but there were limited effects on slow-twitch muscles and muscle fiber type composition. These data provide important evidence of the benefits of exercising paralyzed limbs after SCI. Muscle Nerve, 2016 Muscle Nerve 55: 232-242, 2017.

Gait recovery following spinal cord injury in mice: Limited effect of treadmill training.

BACKGROUND: Several studies in rodents with complete spinal cord transections have demonstrated that treadmill training improves stepping movements. However, results from studies in incomplete spinal cord injured animals have been conflicting and questions regarding the training dosage after injury remain unresolved. OBJECTIVES: To assess the effects of treadmill-training regimen (20 minutes daily, 5 days a week) for 3, 6 or 9 weeks on the recovery of locomotion in hemisected SCI mice. METHODS: A randomized and blinded controlled experimental trial used a mouse model of incomplete spinal cord injury (SCI). After a left hemisection at T10, adult male mice were randomized to trained or untrained groups. The trained group commenced treadmill training one week after surgery and continued for 3, 6 or 9 weeks. Quantitative kinematic gait analysis was used to assess the spatiotemporal characteristics of the left hindlimb prior to injury and at 1, 4, 7 and 10 weeks post-injury. RESULTS: One week after injury there was no movement of the left hindlimb and some animals dragged their foot. Treadmill training led to significant improvements in step duration, but had limited effect on the hindlimb movement pattern. Locomotor improvements in trained animals were most evident at the hip and knee joints whereas recovery of ankle movement was limited, even after 9 weeks of treadmill training. CONCLUSION: These results demonstrate that treadmill training may lead to only modest improvement in recovery of hindlimb movement after incomplete spinal cord injury in mice.

PEA-CLARITY: 3D molecular imaging of whole plant organs.

Here we report the adaptation of the CLARITY technique to plant tissues with addition of enzymatic degradation to improve optical clearing and facilitate antibody probe penetration. Plant-Enzyme-Assisted (PEA)-CLARITY, has allowed deep optical visualisation of stains, expressed fluorescent proteins and IgG-antibodies in Tobacco and Arabidopsis leaves. Enzyme treatment enabled penetration of antibodies into whole tissues without the need for any sectioning of the material, thus facilitating protein localisation of intact tissue in 3D whilst retaining cellular structure.

Exercise training after spinal cord injury selectively alters synaptic properties in neurons in adult mouse spinal cord.

Following spinal cord injury (SCI), anatomical changes such as axonal sprouting occur within weeks in the vicinity of the injury. Exercise training enhances axon sprouting; however, the exact mechanisms that mediate exercised-induced plasticity are unknown. We studied the effects of exercise training after SCI on the intrinsic and synaptic properties of spinal neurons in the immediate vicinity (<2 segments) of the SCI. Male mice (C57BL/6, 9-10 weeks old) received a spinal hemisection (T10) and after 1 week of recovery, they were randomized to trained (treadmill exercise for 3 weeks) and untrained (no exercise) groups. After 3 weeks, mice were killed and horizontal spinal cord slices (T6-L1, 250 µm thick) were prepared for visually guided whole cell patch clamp recording. Intrinsic properties, including resting membrane potential, input resistance, rheobase current, action potential (AP) threshold and after-hyperpolarization (AHP) amplitude were similar in neurons from trained and untrained mice (n=67 and 70 neurons, respectively). Neurons could be grouped into four categories based on their AP discharge during depolarizing current injection; the proportions of tonic firing, initial bursting, single spiking, and delayed firing neurons were similar in trained and untrained mice. The properties of spontaneous excitatory synaptic currents (sEPSCs) did not differ in trained and untrained animals. In contrast, evoked excitatory synaptic currents recorded after dorsal column stimulation were markedly increased in trained animals (peak amplitude 78.9±17.5 vs. 42.2±6.8 pA; charge 1054±376 vs. 348±75 pA·ms). These data suggest that 3 weeks of treadmill exercise does not affect the intrinsic properties of spinal neurons after SCI; however, excitatory synaptic drive from dorsal column pathways, such as the corticospinal tract, is enhanced.

A horizontal slice preparation for examining the functional connectivity of dorsal column fibres in mouse spinal cord.

In spinal cord injury (SCI) research, axon regeneration across spinal lesions is most often assessed using anatomical methods. It would be extremely advantageous, however, to examine the functional synaptic connectivity of regenerating fibres, using high-resolution electrophysiological methods. We have therefore developed a mouse horizontal spinal cord slice preparation that permits detailed analysis of evoked dorsal column (DCol) synaptic inputs on spinal neurons, using whole-cell patch clamp electrophysiology. This preparation allows us to characterise postsynaptic currents and potentials in response to electrical stimulation of DCol fibres, along with the intrinsic properties of spinal neurons. In addition, we demonstrate that low magnification calcium imaging can be used effectively to survey the spread of excitation from DCol stimulation in horizontal slices. This preparation is a potentially valuable tool for SCI research where confirmation of regenerated, functional synapses across a spinal lesion is critical.

The role of propriospinal interneurons in recovery from spinal cord injury.

Over one hundred years ago, Sir Charles Sherrington described a population of spinal cord interneurons (INs) that connect multiple spinal cord segments and participate in complex or 'long' motor reflexes. These neurons were subsequently termed propriospinal neurons (PNs) and are known to play a crucial role in motor control and sensory processing. Recent work has shown that PNs may also be an important substrate for recovery from spinal cord injury (SCI) as they contribute to plastic reorganisation of spinal circuits. The location, inter-segmental projection pattern and sheer number of PNs mean that after SCI, a significant number of them are capable of 'bridging' an incomplete spinal cord lesion. When these properties are combined with the capacity of PNs to activate and coordinate locomotor central pattern generators (CPGs), it is clear they are ideally placed to assist locomotor recovery. Here we summarise the anatomy, organisation and function of PNs in the uninjured spinal cord, briefly outline the pathophysiology of SCI, describe how PNs contribute to recovery of motor function, and finally, we discuss the mechanisms that underlie PN plasticity. We propose there are two major challenges for PN research. The first is to learn more about ways we can promote PN plasticity and manipulate the 'hostile' micro-environment that limits regeneration in the damaged spinal cord. The second is to study the cellular/intrinsic properties of PNs to better understand their function in both the normal and injured spinal cord. This article is part of a Special Issue entitled 'Synaptic Plasticity & Interneurons'.

Down-regulated striatal gene expression for synaptic plasticity-associated proteins in addiction and relapse vulnerable animals.

Reducing the likelihood of relapse represents one of the greatest obstacles in the successful treatment of cocaine addiction. Dysregulation of the synaptic plasticity processes long-term potentiation (LTP) and long-term depression (LTD) is thought to be associated with protracted relapse risk. To improve our understanding of the molecular mechanisms contributing to relapse vulnerability we trained rats (n=52) to self-administer cocaine and phenotyped animals as relapse-vulnerable or relapse-resilient using procedures adapted from Deroche-Gamonet et al. (Science 2004, 305, 1014-1017). Gene expression analysis, targeted at synaptic plasticity-related genes, revealed significant transcript down-regulation in the ventral and dorsal striatum of relapse-vulnerable animals compared to relapse-resilient controls. This included reduced expression of genes encoding proteins implicated in the dendritic translation of synaptic plasticity-related transcripts, the dynamic regulation and trafficking of ionotropic glutamate receptors important for LTP and LTD, along with neuronal surface receptors that initiate downstream signalling pathways associated with synaptic plasticity. Together, our data are consistent with recent reports of an inability to evoke LTD in the striatum of addiction-vulnerable rats. To our knowledge, this is the first study to demonstrate down-regulated synaptic plasticity-associated gene expression not only in the ventral striatum, where the majority of addiction-related synaptic plasticity studies have been conducted, but also in the dorsal striatum of animals categorized as relapse-vulnerable. As these neural correlates were elucidated using an approach incorporating individual behavioural differences, they potentially provide more relevant insight into addiction and assist the development of novel pharmacotherapies to treat relapse.

Cocaine- and amphetamine-regulated transcript (CART) signaling within the paraventricular thalamus modulates cocaine-seeking behaviour.

BACKGROUND: Cocaine- and amphetamine-regulated transcript (CART) has been demonstrated to play a role in regulating the rewarding and reinforcing effects of various drugs of abuse. A recent study demonstrated that i.c.v. administration of CART negatively modulates reinstatement of alcohol seeking, however, the site(s) of action remains unclear. We investigated the paraventricular thalamus (PVT) as a potential site of relapse-relevant CART signaling, as this region is known to receive dense innervation from CART-containing hypothalamic cells and to project to a number of regions known to be involved in mediating reinstatement, including the nucleus accumbens (NAC), medial prefrontal cortex (mPFC) and basolateral amygdala (BLA). METHODOLOGY/PRINCIPAL FINDINGS: Male rats were trained to self-administer cocaine before being extinguished to a set criterion. One day following extinction, animals received intra-PVT infusions of saline, tetrodotoxin (TTX; 2.5 ng), CART (0.625 µg or 2.5 µg) or no injection, followed by a cocaine prime (10 mg/kg, i.p.). Animals were then tested under extinction conditions for one hour. Treatment with either TTX or CART resulted in a significant attenuation of drug-seeking behaviour following cocaine-prime, with the 2.5 µg dose of CART having the greatest effect. This effect was specific to the PVT region, as misplaced injections of both TTX and CART resulted in responding that was identical to controls. CONCLUSIONS/SIGNIFICANCE: We show for the first time that CART signaling within the PVT acts to inhibit drug-primed reinstatement of cocaine seeking behaviour, presumably by negatively modulating PVT efferents that are important for drug seeking, including the NAC, mPFC and BLA. In this way, we identify a possible target for future pharmacological interventions designed to suppress drug seeking.

Measurement of the vertebral canal dimensions of the neck of the rat with a comparison to the human.

The aim of this study was to determine the dimensions of the vertebral canal in the neck of the rat, because little is known about the morphology of the rat's cervical spine. A comparison then was made to the vertebral canal in the neck of the human. In part 1 of this study, we determined the precision of three different methods to measure the vertebral canal. The error (coefficient of variation) in these methods was found to range from 1 to 8%. In part 2, we used a computer-based system to measure digital images of the vertebra and determined the anterior to posterior and the transverse vertebral canal dimensions in the neck of 19 young adult Sprague-Dawley rats. The anterior to posterior dimension of the vertebral canal was greatest at the upper cervical (C1-C2) level and progressively decreased in the more caudal segments (C3-T1). The transverse dimension was greatest at the atlas (C1) vertebra and smallest at the axis (C2) vertebra with a steady increase in the transverse dimension with more caudal segments and a maximum transverse dimension at the level of the C6 and C7 vertebra. This study has demonstrated that the vertebral canal in the neck of young adult rats is similar in some regards to that of human. However, there are clear differences between the rat and human. These may be associated with differences in the morphology of the spinal cord or postural differences such as the cervicothoracic lordosis in bipeds compared with that in quadrupeds.