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Cell cultures play a crucial role in neuroscience research, facilitating the elucidation of the complexities of cellular physiology and pathology. The relative simplicity in producing cultures and the accessibility to cells that the cultures provide, in contrast to in vivo settings, allow users to manipulate and monitor cells more easily at higher throughputs and lower costs. These are ideal for screening purposes and electrophysiological characterizations. Despite the prevalence of methodologies for producing brain cultures from various animal models, rodents in particular, approaches for culturing neurons (and glia) from birds are less established or completely absent as in the case of the Japanese quail model. Here, we present a unique culturing protocol for brain cells (e.g., neurons at different maturation levels, such as progenitor cells, excitatory and inhibitory neurons, microglia, and endothelial cells) from entire forebrains of Japanese quail embryos for high-throughput screening of viral vectors in vitro and other various purposes. Following dissection and digestion methods uniquely suited for avian brains, we tailored the growth media and culturing surface to allow the survival of quail brain cultures for more than three weeks in vitro.

Abstract White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0–3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.

ABSTRACT: This review is a summary of a Poultry Science Association symposium addressing myopathies in broilers’ breast meat, focusing on the interactions between genetics, nutrition, husbandry, and meat processing. The Pectoralis major myopathies (woody breast [WB]; white striping [WS]; spaghetti meat [SM]) and Pectoralis minor (“feathering”) are described, followed by discussing their prevalence, potential causes, current and future ways to mitigate, as well as detection methods (in live birds and meat) as well as ways to utilize affected meat. Overall, breast myopathies remain an important focus across the poultry industry and whilst a lot of data and knowledge has been gathered, it is clear that there is still a lot to understand. As there are multiple factors impacting the occurrence of breast myopathies, their reduction relies on a holistic approach. Ongoing balanced breeding strategies by poultry breeders is targeting the longer-term genetic component but comprehending the significant influence from nongenetic factors (short-term solutions such as nutrition) remains a key area of opportunity. Consequently, understanding the physiology and biological needs of the muscle through the life of the bird is critical to reduce the myopathies (e.g., minimizing oxidative stress) and gain more insight into their etiology.

ABSTRACT: A lean meat batter system was mixed with four plant proteins at 3, 6, 9, and 12% (w/w): pea protein A (PA), pea protein B (PB), brown rice protein (BR) and faba bean protein (FB). Texture profile analysis (TPA) revealed that increasing plant protein levels hardened the hybrid meat batters, with PA and PB leading to the hardest gels. TPA results were supported by micrographs, demonstrating that the two pea proteins formed large aggregates, contributing to a firmer hybrid meat gel. Dynamic rheology showed that the incorporation of plant proteins lowered the storage modulus (G') during the heating stage (20 to 72°C), yet the 6% PA treatment produced a final G' (after cooling) closest to the control (CL). Nuclear Magnetic Resonance (NMR) T2 relaxometry also demonstrated that plant proteins reduced the water mobility in hybrid meat batters. Results were in line with the cooking loss, except for a higher cooking loss in the BR formulation compared to the CL. Color measurement showed that increasing plant protein levels led to darker and yellower meat batters; however, the effect on redness varied among treatments. Overall, the findings suggest that pea proteins have superior functionality and compatibility within a lean poultry meat protein system, compared to BR and FB tested here.

Abstract The current consensus holds that optically‐cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue‐clearing techniques relying on the latter's ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI‐contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non‐delipidating clearing methods can produce MRI‐compatible specimens or whether MRI‐contrast can be re‐established. These limitations hinder the development of multimodal MRI‐light‐microscopy (LM) imaging approaches. This study assesses the relation between MRI‐contrast, and delipidation in optically‐cleared whole brains following different tissue‐clearing approaches. It is demonstrated that uDISCO and ECi‐brains are MRI‐compatible upon tissue rehydration, despite both methods’ substantial delipidating‐nature. It is also demonstrated that, whereas Scale‐clearing preserves most lipids, Scale‐cleared brain lack MRI‐contrast. Furthermore, MRI‐contrast is restored to lipid‐free CLARITY‐brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI‐contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI‐contrast. These findings then enabled us to develop a multimodal MRI‐LM‐imaging approach, opening new avenues to bridge between the micro‐ and mesoscale for biomedical research and clinical applications.

ABSTRACT: In the current scientific literature, one can find >100 different methods to evaluate water-holding capacity in fresh and cooked meat. The main concepts are based on removing some of the water by either gravity, application of pressure (e.g., centrifugal force), and heating while measuring water exudate to predict the water holding capacity (WHC) during storage, processing, cooking, and/or distribution. More sophisticated methods include nuclear magnetic resonance (NMR) in which the relaxation of water molecules within a meat protein/gel system is measured to predict how the water (75% in lean meat) will behave during processing. Overall, the number of tests reported is also so high because there are quite big variations in test conditions (e.g., 750–30,000 g for centrifugal testing). The aim of this article (outcome of a symposium on methods for poultry meat characterization) is to help the reader navigate through the different setups and suggest standardized testing based on scientific principles. The recommended WHC test is the application of low centrifugal force (750 g so sample is not permanently deformed) to a protein gel, while the sample is placed on a screen platform to avoid reabsorbing the liquid separating during the slowing down of the centrifuge. It is also recognized that some meat samples (e.g., high in fat) might require a different g-force, so it is recommended to employ both the conditions mentioned above and the lab-specific conditions. Our overall goal should always be to increase uniformity in test procedures, which will enhance our capabilities to compare results among research groups.

Co extrusion sausage technology has been a game changer in the industry as it has transformed the traditional way of filling meat betters into premade casings (e.g., synthetic materials such as cellulose or natural casings) to producing the casings on top of the meat batter as it comes out of the stuffer. This allows full automation of the process (working 24/7) with lower waste, while also increasing food safety standards. The main material used is collagen which today is extracted from a limited type of beef hides. It is then treated with a strong alkaline solution, to breakdown some of the original structures, and later with a strong acid to allow swelling of the resulting suspension. The application of the collagen gel requires special equipment to line up the collagen fibers in such a way that they provide the strength and elasticity during the cooking operation (meat expends during cooking) and later provide the consumer with the characteristics bit/“snap” similar to natural casings. Understanding the interactions between the chemical and physical properties of collagen is essential in obtaining good results. During production it is important that the collagen is quickly dried and crosslinked so the shape of the product will not be modified. This requires special large horizontal dryers and a unit to apply liquid smoke (source of aldehydes for crosslinking). Currently most systems are built for large capacity production, and therefore require large investment, however the industry is working on developing smaller and more flexible units for future use.

Abstract Open information about government organizations should interest all citizens who care about their governments’ functionality. Large-scale open governmental data open new opportunities for citizens and researchers to monitor their government’s activities and improve its transparency. Over the years, various projects and systems have processed and analyzed governmental data based on open government information. Here, we present the Collecting and Analyzing Parliament Data (CAPD) framework. This novel generic open framework enables collecting and analyzing large-scale public governmental data from multiple sources. This study utilized our framework to collect over 64,000 parliament protocols from over 90 committees from three countries and analyzed it to calculate structured features. Next, we utilized anomaly detection and time series analysis to achieve a number of insights into the committees’ activities. This study demonstrates that the CAPD framework can be utilized to effectively identify anomalous meetings and detect dates of events that affect the parliaments’ functionality and help to monitor their activities.

Abstract Autism is a neurodevelopmental disorder characterized by early-onset social behavioral deficits and repetitive behaviors. Chromodomain helicase DNA-binding protein (CHD8) is among the genes most strongly associated with autism. In addition to the core behavioral symptoms of autism, affected individuals frequently present with gastrointestinal symptoms that are also common among individuals harboring mutations in the gene encoding CHD8. However, little is known regarding the mechanisms whereby CHD8 affects gut function. In addition, it remains unknown whether gastrointestinal manifestations contribute to the behavioral phenotypes of autism. The current study found that mice haploinsufficient for the large isoform of Chd8 (Chd8L) exhibited increased intestinal permeability, transcriptomic dysregulation in gut epithelial cells, reduced tuft cell and goblet cell counts in the gut, and an overall increase in microbial load. Gut epithelial cell-specific Chd8 haploinsufficiency was associated with increased anxiety-related behaviors together with a decrease in tuft cell numbers. Antibiotic treatment of Chd8L haploinsufficient mice attenuated social behavioral deficits. Together, these results suggest Chd8 as a key determinant of autism-related gastrointestinal deficits, while also laying the ground for future studies on the link between GI deficits and autism-related behaviors.

Abstract Multiplexed imaging enables measurement of multiple proteins in situ, offering an unprecedented opportunity to chart various cell types and states in tissues. However, cell classification, the task of identifying the type of individual cells, remains challenging, labor-intensive, and limiting to throughput. Here, we present CellSighter, a deep-learning based pipeline to accelerate cell classification in multiplexed images. Given a small training set of expert-labeled images, CellSighter outputs the label probabilities for all cells in new images. CellSighter achieves over 80% accuracy for major cell types across imaging platforms, which approaches inter-observer concordance. Ablation studies and simulations show that CellSighter is able to generalize its training data and learn features of protein expression levels, as well as spatial features such as subcellular expression patterns. CellSighter’s design reduces overfitting, and it can be trained with only thousands or even hundreds of labeled examples. CellSighter also outputs a prediction confidence, allowing downstream experts control over the results. Altogether, CellSighter drastically reduces hands-on time for cell classification in multiplexed images, while improving accuracy and consistency across datasets.

Multi-modal imaging, by light-microscopy (LM) and Magnetic Resonance Imaging (MRI), holds promise for examining the brain across various resolutions and scales. While MRI acquires images in three dimensions, acquisition of intact whole-brain by LM requires a process of tissue clearing that renders the brain transparent. Removal of lipids (delipidation) is a critical step in the tissue clearing process, and was previsouly suggested to be the cause for absence of MRI contrast in cleared brains. Yet, the association between MRI contrast, delipidation and the different clearing techniques is debatable. Here, we provide datasets concerning lipid-content in cleared brain tissues obtained by various approaches. Fixed mouse and rat brains were cleared by CLARITY, Scale, uDISCO and ECi clearing techniques. Lipid-content was assessed at various intermediate steps of the different clearing methods, as well as at the end of the processes. Methods employed included whole brain MRI acquisition, Oil Red O (ORO)- and carbocyanine DiI-staining of cryosections, and DiI-washout assay from brain slices. MRI contrast-to-noise ratio, staining intensities and integrity of tissue were systematically analyzed. We demonstrate that lipid electrophoresis, an essential step of the CLARITY approach, engenders progressive reduction in MRI contrast in non-cleared (PFA-fixed) control brains, as well as strongly reduces contrast from uDISCO and ECi-cleared brains. ORO minimally stained CLARITY-cleared brains, however efficiently labelled uDISCO and ECi-cleared brains. Conversely, and in contrast to ORO-staining, DiI equally stained control, CLARITY, ECi and uDISCO-cleared brains. Both ORO- and DiI-staining demonstrated impairment in brain tissue integrity following CLARITY, but less so in uDISCO and ECi brains. DiI-washout assay demonstrated that each of the solvents employed along the process of uDISCO and ECi are highly delipidating, as well as the SDS-electrophoresis employed during CLARITY clearing. However, Scale treatment preserved most of the DiI dye. These data emphasize the variability in lipid assessment of cleared tissues by common techniques, and may help to resolve the contribution of lipids in brain MRI contrast.

Acute gastrointestinal infection with intracellular pathogens like Salmonella Typhimurium triggers the release of the proinflammatory cytokine interleukin 1β (IL-1β). However, the role of IL-1β in intestinal defense against Salmonella remains unclear. Here, we show that IL-1β production is detrimental during Salmonella infection. Mice lacking IL-1β (IL-1β -/-) failed to recruit neutrophils to the gut during infection, which reduced tissue damage and prevented depletion of short-chain fatty acid (SCFA)-producing commensals. Changes in epithelial cell metabolism that typically support pathogen expansion, such as switching energy production from fatty acid oxidation to fermentation, were absent in infected IL-1β -/- mice which inhibited Salmonella expansion. Additionally, we found that IL-1β induces expression of complement anaphylatoxins and suppresses the complement-inactivator carboxypeptidase N (CPN1). Disrupting this process via IL-1β loss prevented mortality in Salmonella-infected IL-1β -/- mice. Finally, we found that IL-1β expression correlates with expression of the complement receptor in patients suffering from sepsis, but not uninfected patients and healthy individuals. Thus, Salmonella exploits IL-1β signaling to outcompete commensal microbes and establish gut colonization. Moreover, our findings identify the intersection of IL-1β signaling and the complement system as key host factors involved in controlling mortality during invasive Salmonellosis.

Forward Brillouin scattering fiber sensors can detect and analyze media outside the cladding of standard fibers, where guided light does not reach. Nearly all such sensors reported to-date have relied on the radially symmetric guided acoustic modes of the fiber. Wave motion in these modes is strictly dilatational. However, forward Brillouin scattering also takes place through torsional–radial guided acoustic modes of the fiber. Torsional–radial modes exhibit more complex tensor characteristics, and they consist of both dilatational and shear wave contributions. In this work, we show that forward Brillouin sensing through torsional–radial acoustic modes is qualitatively different from processes based on the radial ones. While dilatational wave components may dissipate toward liquids outside the fiber cladding, shear waves do not. Consequently, the effect of outside liquids varies among torsional–radial modes. Those modes that are dominated by their dilatational components undergo faster decay rates, whereas other modes with large shear contributions decay at much slower rates in the same liquid. The difference in decay rates may reach a factor of seven. Experimental observations are well supported by the analysis. The differences among modes are also found with liquid outside specific coating layers. Large changes in decay rates are observed when a phase transition between solid and liquid occurs outside the cladding boundary. The monitoring of multiple mode categories provides more complete assessment of outside media and enhances the capabilities of forward Brillouin scattering fiber sensors.

AAV1-T593K (AAV1*) is a custom-made viral vector that enables efficient transduction and manipulation of quail neurons, thereby expanding the toolkit for avian neuroscience research.

ABSTRACT: The aims of this study were to i) estimate the occurrence of pale, soft, and exudative (PSE) meat in modern commercial Ontario broiler flocks, ii) determine the effects of the chilling method (water vs. air) on PSE meat, and iii) investigate a new inexpensive colorimeter (10% of the price of traditional color meters), the Nix Color Sensor, as an objective color measurement of chicken meat. Between June 2019 to March 2020, a total of 17 different broiler flocks were processed. The color of 1,700 boneless skinless Pectoralis major muscles was randomly measured (100/flock), where 255 samples were also measured for pH, water-holding capacity (WHC), cooking loss, and penetration force. In addition, a traditional Minolta colorimeter was used to measure random 95 samples from a single water-chilled flock and subsequently compared the values obtained with the Nix Color Sensor. Strong correlations of L* values (rho = 0.75; P < 0.001), a* values (rho = 0.72; P < 0.001), and b* values (rho = 0.80; P < 0.001) were observed. When an L* value of 43 was used as the cut-off for the Nix, 12.5% of fillets were classified as PSE meat. Statistical differences (P < 0.05) were observed between the air and water-chill methods for L*, pH, and WHC. However, there were no significant differences observed between the 2 methods for cooking loss and penetration force values. The study indicated that PSE meat is still a challenge in Ontario broilers, and that the L*, pH, and WHC of breast meat (all indicate meat quality) are affected by the chilling method. In addition, the Nix was found to be an affordable, objective, and convenient sensor for measuring chicken meat color.

Over the past decade, significant progress in quantum technologies has been made, and hence, engineering of these systems has become an important research area. Many researchers have become interested in studying ways in which classical integrated circuits can be used to complement quantum mechanical systems, enabling more compact, performant, and/or extensible systems than would be otherwise feasible. In this article—written by a consortium of early contributors to the field—we provide a review of some of the early integrated circuits for the quantum information sciences. Complementary metal--oxide semiconductor (CMOS) and bipolar CMOS (BiCMOS) integrated circuits for nuclear magnetic resonance, nitrogen-vacancy-based magnetometry, trapped-ion-based quantum computing, superconductor-based quantum computing, and quantum-dot-based quantum computing are described. In each case, the basic technological requirements are presented before describing proof-of-concept integrated circuits. We conclude by summarizing some of the many open research areas in the quantum information sciences for CMOS designers.

Abstract Robustness can refer to an animal’s ability to overcome perturbations. Intense selection for production traits in livestock has resulted in reduced robustness which has negative implications for livability as well as production. There is increasing emphasis on improving robustness through poultry breeding, which may involve identifying novel phenotypes that could be used in selection strategies. The hypothalamic–pituitary–adrenal (HPA) axis and associated hormones (e.g., corticosterone) participate in many metabolic processes that are related to robustness. Corticosterone can be measured non-invasively in feathers (FCORT) and reflects the average HPA axis activity over the feather growing period, however measurement is expensive and time consuming. Fault bars are visible feather deformities that may be related to HPA axis activity and may be a more feasible indicator trait. In this study, we estimated variance components for FCORT and fault bars in a population of purebred turkeys as well as their genetic and partial phenotypic correlations with other economically relevant traits including growth and efficiency, carcass yield, and meat quality. The estimated heritability for FCORT was 0.21 ± 0.07 and for the fault bar traits (presence, incidence, severity, and index) estimates ranged from 0.09 to 0.24. The genetic correlation of FCORT with breast weight, breast meat yield, fillet weight, and ultimate pH were estimated at −0.34 ± 0.21, −0.45 ± 0.23, −0.33 ± 0.24, and 0.32 ± 0.24, respectively. The phenotypic correlations of FCORT with breast weight, breast meat yield, fillet weight, drum weight, and walking ability were −0.16, −0.23, −0.18, 0.17, and 0.21, respectively. Some fault bar traits showed similar genetic correlations with breast weight, breast meat yield, and walking ability but the magnitude was lower than those with FCORT. While the dataset is limited and results should be interpreted with caution, this study indicates that selection for traits related to HPA axis activity is possible in domestic turkeys. Further research should focus on investigating the association of these traits with other robustness-related traits and how to potentially implement these traits in turkey breeding.

As the use of magnetic resonance imaging of the fetal brain has evolved, the need to understand its efficiency in the biometry of the fetal brain has broadened. This study aimed to assess the level of agreement and correlation between the two cardinal imaging methods of fetal neuroimaging, ultrasonography (US) and magnetic resonance imaging (MRI), by measuring the corpus callosum (CC) and transverse cerebellar diameter (TCD) in terms of length and percentile. Measurements of CC and TCD length and percentile were documented over a 7-year span in a tertiary referral medical center. All US and MRI examinations were performed in the customary planes and subcategorized by valid reference charts. Exclusion and inclusion criteria were set before the collection and processing of the data. A total of 156 fetuses out of 483 were included in the study. A positive, strong correlation and agreement were found (r = 0.78; ICC = 0.76) between US and MRI in TCD measurements. For CC length measurement, a moderate correlation and moderate agreement (r = 0.51; ICC = 0.49) between US and MRI was observed. TCD and CC percentiles had lower levels of correlation and agreement compared with the length variables. Our study indicates good agreement between MRI and US in the assessment of TCD measurement as a part of antenatal neuroimaging. Furthermore, while the two techniques are not always compatible, they are complementary methods.

Spaghetti meat (SM) and woody breast (WB) are breast muscle myopathies of broiler chickens, characterized by separation of myofibers and by fibrosis, respectively. This study sought to investigate the transcriptomic profiles of breast muscles affected by SM and WB. Targeted sampling was conducted on a flock to obtain 10 WB, 10 SM, and 10 Normal Pectoralis major muscle samples from 37-day-old male chickens. Total RNA was extracted, cDNA was used for pair-end sequencing, and differentially expressed genes (DEGs) were determined by a false discovery rate of 1.5-fold change. Principal component and heatmap cluster analyses showed that the SM and WB samples clustered together. No DEGs were observed between SM and WB fillets, while a total of 4018 and 2323 DEGs were found when comparing SM and WB, respectively, against Normal samples. In both the SM and WB samples, Gene Ontology terms associated with extracellular environment and immune response were enriched. The KEGG analysis showed enrichment of cytokine–cytokine receptor interaction and extracellular matrix–receptor interaction pathways in both myopathies. Although SM and WB are macroscopically different, the similar transcriptomic profiles suggest that these conditions may share a common pathogenesis. This is the first study to compare the transcriptomes of SM and WB, and it showed that, while both myopathies had profiles different from the normal breast muscle, SM and WB were similar, with comparable enriched metabolic pathways and processes despite presenting markedly different macroscopic features.

The effects of salt-sensitive alginate (“A”) and a two-component salt-tolerant alginate system (“B”) used at a 0.5% or 1.0% level were evaluated in normal breast (NB) chicken fillets and in spaghetti meat (SM) fillets. Minced raw and cooked SM samples showed higher cooking loss (p < 0.05) and lower penetration force compared to NB meat. Both alginate systems significantly raised the penetration force in raw samples and decreased cooking loss (p < 0.05). Adding 1% of “A” or 0.5% “B” to SM, without salt, resulted in a similar penetration force as the cooked NB meat, while 1% “B” with salt resulted in a higher penetration force. Excluding salt from SM samples while adding alginate “A” or “B” improved texture profiles, but not to the same level as using NB without additives. Overall, salt, together with alginate “B”, improved the texture of SM to that of normal meat without myopathy.

ABSTRACT: Plant fiber addition (citrus A and B, apple, pea, bamboo, and sugar cane) to lean turkey meat was evaluated and texture, yield, and microstructure were compared to a control. The best 2 were the sugar cane and apple peel fibers which reduced cooking loss, and increased hardness by 20% compared to the control. The bamboo fibers significantly improved hardness but not yield, while the citrus A and apple fibers reduced cooking loss but did not affect hardness. The differences in the effect of fiber type on texture appear to be related to their origin (e.g., sugar cane and bamboo originating from large plants requiring strong fibers, compared citrus and apple fruits), and fiber length determined by the fiber extraction procedure.