Miracle-dz/UniFAR-FTUs huggingface dataset:
Avian leukosis virus subgroup J and reticuloendotheliosis virus coinfection induced TRIM62 regulation of the actin cytoskeleton

Background Coinfection with avian leukosis virus subgroup J (ALV-J) and reticuloendotheliosis virus (REV) is common in chickens, and the molecular mechanism of the synergistic pathogenic effects of the coinfection is not clear. Exosomes have been identified as new players in the pathogenesis of retroviruses. The different functions of exosomes depend on their cargo components. Objectives The aim of this study was to investigate the function of co-regulation differentially expressed proteins in exosomes on coinfection of ALV-J and REV. Methods Here, viral replication in CEF cells infected with ALV-J, REV or both was detected by immunofluorescence microscopy. Then, we analyzed the exosomes isolated from supernatants of chicken embryo fibroblast (CEF) cells single infected and coinfected with ALV-J and REV by mass spectrometry. KEGG pathway enrichment analyzed the co-regulation differentially expressed proteins in exosomes. Next, we silenced and overexpressed tripartite motif containing 62 (TRIM62) to evaluate the effects of TRIM62 on viral replication and the expression levels of NCK-association proteins 1 (NCKAP1) and actin-related 2/3 complex subunit 5 (ARPC5) determined by quantitative reverse transcription polymerase chain reaction. Results The results showed that coinfection of ALV-J and REV promoted the replication of each other. Thirty proteins, including TRIM62, NCK-association proteins 1 (NCKAP1, also known as Nap125), and Arp2/3-5, ARPC5, were identified. NCKAP1 and ARPC5 were involved in the actin cytoskeleton pathway. TRIM62 negatively regulated viral replication and that the inhibition of REV was more significant than that on ALV-J in CEF cells coinfected with TRIM62. In addition, TRIM62 decreased the expression of NCKAP1 and increased the expression of ARPC5 in coinfected CEF cells. Conclusions Collectively, our results indicated that coinfection with ALV-J and REV competitively promoted each other's replication, the actin cytoskeleton played an important role in the coinfection mechanism, and TRIM62 regulated the actin cytoskeleton.
A Framework for Optimizing High-Content Imaging of 3D Models for Drug Discovery

Three-dimensional (3D) spheroid models are rapidly gaining favor for drug discovery applications due to their improved morphological characteristics, cellular complexity, long lifespan in culture, and higher physiological relevance relative to two-dimensional (2D) cell culture models. High-content imaging (HCI) of 3D spheroid models has the potential to provide valuable information to help researchers untangle disease pathophysiology and assess novel therapies more effectively. The transition from 2D monolayer models to dense 3D spheroids in HCI applications is not trivial, however, and requires 3D-optimized protocols, instrumentation, and resources. Here, we discuss considerations for moving from 2D to 3D models and present a framework for HCI and analysis of 3D spheroid models in a drug discovery setting. We combined scaffold-free, multicellular spheroid models with scalable, automation-compatible plate technology enabling image-based applications ranging from high-throughput screening to more complex, lower-throughput microphysiological systems of organ networks. We used this framework in three case studies: investigation of lipid droplet accumulation in a human liver nonalcoholic steatohepatitis (NASH) model, real-time immune cell interactions in a multicellular 3D lung cancer model, and a high-throughput screening application using a 3D co-culture model of gastric carcinoma to assess dose-dependent drug efficacy and specificity. The results of these proof-of-concept studies demonstrate the potential for high-resolution image-based analysis of 3D spheroid models for drug discovery applications, and confirm that cell-level and temporal-spatial analyses that fully exploit multicellular features of spheroid models are not only possible but soon will be routine practice in drug discovery workflows.
Coronaviridae—Old friends, new enemy!

Abstract Coronaviridae is a family of single‐stranded positive enveloped RNA viruses. This article aimed to review the history of these viruses in the last 60 years since their discovery to understand what lessons can be learned from the past. A review of the PubMed database was carried out, describing taxonomy, classification, virology, genetic recombination, host adaptation, and main symptoms related to each type of virus. SARS‐CoV‐2 is responsible for the ongoing global pandemic, and SARS‐CoV and MERS‐CoV were responsible for causing severe respiratory illness and regional epidemics in the past while the four other strains of CoVs (229‐E OC43, NL63, and HKU1) circulate worldwide and normally only cause mild upper respiratory tract infections. Given the enormous diversity of coronavirus viruses in wildlife and their continuous evolution and adaptation to humans, future outbreaks would undoubtedly occur. Restricting or banning all trade in wild animals in wet markets would be a necessary measure to reduce future zoonotic infections.
Allometry in the Bearded Dragon Pogona barbata (Sauria: Agamidae): Sex and Geographic Differences

Allometry in size and shape between sexes was investigated in preserved Bearded Dragon Pogona barbata museum specimens. Measurements for snout-vent, head, leg and tail lengths were obtained from 236 individuals ranging from hatchlings to large adults. Juveniles and adults were sexed, and size at onset of maturity was determined. Geographic variation in P. barbata was also studied by comparing lizards from three regions in New South Wales (NSW), which differ in annual rainfall.Relative to snout-vent length, head and leg lengths were in negative allometry in all specimens, and tail length was in positive allometry in juveniles, but negative in adults. Sexual dimorphism was evident in body size and shape. Males grew larger and reached maturity at larger sizes than females. While juvenile shape did not differ between the sexes, mature males had proportionately longer heads, legs and tails than adult females. This generalisation in sexual shape dimorphism did not hold true for animals from different NSW region.
Neighborhood Built Environment Measures and Association with Physical Activity and Sedentary Time in 9–14-Year-Old Children in Saskatoon, Canada

This study assessed whether perceptual and researcher-rated measures of neighborhood-built environments (BEs) predict device-based multiple activity-related outcomes, specifically: moderate-to-vigorous physical activity (MVPA), light physical activity (LPA), and sedentary time (ST), in children. Eight hundred and sixteen children aged 9–14 years from Saskatoon, Canada, were surveyed on their perceptions of BE, and their PA outcomes were objectively monitored for one week at three different time frames over a one-year period, September 2014 to August 2015. The researcher-rated BE measures were collected by trained researchers using multiple BE audit tools: neighborhood active living potential (NALP) and Irvine Minnesota inventory (IMI), 2009–2010. A multilevel modeling approach was taken to understand BE influences of children’s PA outcomes. Children’s perceived availability of parks and sidewalks predicted a higher accumulation of MVPA and a lower accumulation of ST. Children’s report of the absence of neighborhood social disorder (e.g., threats from scary dogs/people) predicted a higher LPA, while reported concern about crime predicted a lower MVPA. Researcher-rated neighborhood activity friendliness predicted a lower ST, however, researcher-rated safety from crime predicted a higher ST. Perceived BE characteristic were stronger predictors of children’s PA outcomes compared to researcher-rated BE factors.
Alterations to vestibular morphology in highly bred domestic dogs may affect balance

The modern domestic dog (Canis lupus familiaris) provides an excellent model to examine the effects of cranial modification. Extreme variation in skull length among dog breeds due to high levels of selective breeding is known to be linked to disorders of the head and neck. Such alteration may also influence sensory organs including those of the vestibular system (VS), one of the most fundamental sense organs, essential in maintaining balance. Studies in mammals have shown that orientation of ipsilateral semicircular canals (SCCs) of the VS at right angles (orthogonality) is related to angular acceleration sensitivity. Due to their considerable variation in craniofacial form while exhibiting similar locomotion, domestic dogs provide an excellent natural experiment to examine if cranial alteration influences VS functional morphology. Our methods examine how change in cranial base length across dog breeds relates to SCC orthogonality using linear modeling and analyses of variance. The sample studied (29 bony labyrinths of 17 dog breeds) was obtained from a previous study on canid inner ear metrics. Results support the hypothesis that orthogonality between the anterior and posterior SCC + ampulla significantly correlates with cranial base length. This suggests a close relationship between the orientations of SCCs with their ampullae and cranial structure among dog breeds. Specifically, highly derived breeds, such as the brachycephalic pug, have anterior and posterior SCCs and ampullae that deviate the most from orthogonality. Therefore, such highly bred domestic dogs may also have altered vestibular function due to compressed cranial form.
Phylogeography of North American mountain bromes

Although native grasses are often desired and used for revegetation of disturbed areas, genetic differences may exist within and among natural and cultivated germplasm sources. This phylogeographic study compares geographic origin and genealogical linkages of 25 natural and cultivated germplasm sources of mountain brome (Bromus carinatus Hook. & Arn. [Poaceae]) from western North America. Significant variation among accessions (FST = 0.70) was detected by analysis of molecular variance (AMOVA), based on the number of amplified fragment length polymorphisms (AFLPs) between individual plants. Likewise, significant differences among 4 hierarchical genotypic groups, encompassing all but 5 unique accessions, were also detected (FCT = 0.47). This study identified at least one well-defined genealogical lineage, comprising 8 accessions, distributed over a broad geographic region and different ecosystems of western North America. Two other hierarchical groups, comprising 6 accessions and 3 accessions, were located within or near specific ecoregions. Results of this study indicate that natural genealogical lineages of cultivars, such as Garnet mountain brome, have dispersed and succeeded over broad geographical regions. However, more research and plant material work are needed before specific recommendations can be made over the entire species distribution.
Novel feeding interactions amplify the impact of species redistribution on an Arctic food web

Species are redistributing globally in response to climate warming, impacting ecosystem functions and services. In the Barents Sea, poleward expansion of boreal species and a decreased abundance of Arctic species are causing a rapid borealization of the Arctic communities. This borealization might have profound consequences on the Arctic food web by creating novel feeding interactions between previously non co‐occurring species. An early identification of new feeding links is crucial to predict their ecological impact. However, detection by traditional approaches, including stomach content and isotope analyses, although fundamental, cannot cope with the speed of change observed in the region, nor with the urgency of understanding the consequences of species redistribution for the marine ecosystem. In this study, we used an extensive food web (metaweb) with nearly 2,500 documented feeding links between 239 taxa coupled with a trait data set to predict novel feeding interactions and to quantify their potential impact on Arctic food web structure. We found that feeding interactions are largely determined by the body size of interacting species, although species foraging habitat and metabolic type are also important predictors. Further, we found that all boreal species will have at least one potential resource in the Arctic region should they redistribute therein. During 2014–2017, 11 boreal species were observed in the Arctic region of the Barents Sea. These incoming species, which are all generalists, change the structural properties of the Arctic food web by increasing connectance and decreasing modularity. In addition, these boreal species are predicted to initiate novel feeding interactions with the Arctic residents, which might amplify their impact on Arctic food web structure affecting ecosystem functioning and vulnerability. Under the ongoing species redistribution caused by environmental change, we propose merging a trait‐based approach with ecological network analysis to efficiently predict the impacts of range‐shifting species on food webs.
Generation of cynomolgus monkey fetuses with intracytoplasmic sperm injection based on the MII-stage oocytes acquired by personalized superovulation protocol

Background Mature oocytes at the metaphase II status (MII-stage oocytes) played an important role in assisted reproductive technology in non-human primates. Objectives In order to improve the proportion of MII-stage oocytes retrieval, three different superovulation protocols were performed on 24 female cynomolgus monkeys. Methods All the monkeys received once-daily injection of follicle-stimulating hormone (25 international unit [IU]) on day 3 of the menstruation, 3-day intervals, twice daily for 8–12 days until the time of human chorionic gonadotropin (1,500 IU) injection, on the 14–17th day of menstruation collecting oocytes. The difference between protocol I and protocol II was that 0.1 mg the gonadotropin-releasing hormone agonist was injected on day 1 of the menstruation, while the difference between personalized superovulation protocol and protocol II was that oocytes could be collected on the 14–17th day of menstrual cycle according to the length of each monkey. Results The total number of oocytes harvested using the personalized superovulation protocol was much higher than that using protocol I (p < 0.05), and the proportion of MII-stage oocytes was significantly greater than that from either superovulation protocol I or II (p < 0.001 and p < 0.01 respectively), while the proportion of immature oocytes at the germinal vesicle was less than that from superovulation protocol I (p < 0.05). Conclusions The personalized superovulation protocol could increase the rate of MII-stage oocytes acquired, and successfully develop into embryos after intracytoplasmic sperm injection, and eventually generated fetus.
Imaging Flow Cytometry Analysis of CEACAM Binding to Opa‐Expressing Neisseria gonorrhoeae

Human carcinoembryonic antigen‐related cell adhesion molecules (CEACAMs) are a family of receptors that mediate intercellular interactions. Pathogenic bacteria have ligands that bind CEACAMs on human cells. Neisseria gonorrhoeae (Gc) encodes numerous unique outer membrane opacity‐associated (Opa) proteins that are ligands for one or more CEACAMs. CEACAMs that are expressed on epithelial cells facilitate Gc colonization, while those expressed on neutrophils affect phagocytosis and consequent intracellular survival of Gc. Since Opa protein expression is phase‐variable, variations in receptor tropism affect how individual bacteria within a population interact with host cells. Here we report the development of a rapid, quantitative method for collecting and analyzing fluorescence intensity data from thousands of cells in a population using imaging flow cytometry to detect N‐CEACAM bound to the surface of Opa‐expressing Gc. We use this method to confirm previous findings regarding Opa‐CEACAM interactions and to examine the receptor–ligand interactions of Gc expressing other Opa proteins, as well as for other N‐CEACAM proteins. © 2020 International Society for Advancement of Cytometry
Assembly of Fluorescent Chiral Photonic Crystal Membrane and Its Sensitive Responses with Multiple Signals Induced by Small Molecules.

Chiral liquid crystal materials that are responsive to environmental stimuli are in demand. A chiral photonic crystal membrane based on cellulose nanocrystals (CNCs) was prepared by molecule assembly in the present work. A fluorescent molecule containing a cationic group, [N-(3-N-benzyl-N,N-dimethyl-propyl ammonium chloride)-1,8-naphthalimide] hydrazine (ANH), was assembled on the surface of the CNCs. The new chiral photonic crystal membrane possesses supersensitive multi-responses to small molecules, such as water and formaldehyde molecules. The appearance, liquid crystal texture, fluorescence and color of the chiral membrane have sensitive changes induced by small molecules. With increasing RH from 30% to 100%, the reflectance peak of the membrane red shifted from 498 nm to 736 nm. Especially, the iridescent texture and fingerprint structure of the membrane could change markedly under trace amounts of formaldehyde level, and the chiral membrane can form an extremely sensitive off-on fluorescence switch. The relationship between the fluorescence intensity and the trace concentration of formaldehyde satisfied the linear equation with the association coefficient of 0.9997. The changes in fluorescence and color are visible to the naked eye, and the membrane can quantitatively recognize trace formaldehyde at molecular level in a humid environment. The mechanism by which the fluorescence switch operates was investigated using density functional theory (DFT) at the B3LYP/6-31G (d) level. The membrane has potential for use in the fields of advanced functional materials and biomaterials.
Clinical Validation of a SARS-CoV-2 Real-Time Reverse Transcription PCR Assay Targeting the Nucleocapsid Gene

Abstract Background Detection of SARS-CoV-2 viral RNA is important for the diagnosis and management of COVID-19. Methods We present a clinical validation of a RT-PCR assay for the SARS-CoV-2 nucleocapsid (N1) gene. Offboard lysis on an automated nucleic acid extraction system (EMAG®) was optimized with endemic Coronaviruses (OC43 and NL63). Genomic RNA and SARS-CoV-2 RNA in a recombinant viral protein coat (Accuplex) were used as control materials and compared for recovery from nucleic acid extraction. Results Nucleic acid extraction showed decreased recovery of endemic Coronavirus in vitro transcribed RNA (NL63) compared to attenuated virus (OC43). SARS-CoV-2 RNA (Accuplex) had more reliable recovery from extraction through amplification compared to genomic RNA. Recovery of genomic RNA was improved by combining lysis buffer with clinical matrix prior to adding RNA. The RT-PCR assay demonstrated 100% in silico sensitivity and specificity. The accuracy across samples was 100% (75 of 75). Precision studies showed 100% intra-run, inter-run, and inter-technologist concordance. The limit of detection was 264 copies per ml (estimated 5 copies per reaction; 35.56 mean Ct value). Conclusions This SARS-CoV-2 assay demonstrates appropriate characteristics for use under an emergency use authorization. Endemic Coronavirus controls were useful in optimizing the extraction procedure. In the absence of live or attenuated virus, recombinant virus in a protein coat is an appropriate control specimen type for assay validation during a pandemic.
Polymer Matrix Incorporated with ZIF-8 for Application in Nonlinear Optics

Polymers with embedded metal–organic frameworks (MOFs) have been of interest in research for advanced applications in gas separation, catalysis and sensing due to their high porosity and chemical selectivity. In this study, we utilize specific MOFs with high thermal stability and non-centrosymmetric crystal structures (zeolitic imidazolate framework, ZIF-8) in order to give an example of MOF–polymer composite applications in nonlinear optics. The synthesized MOF-based polymethyl methacrylate (PMMA) composite (ZIF-8–PMMA) demonstrates the possibility of the visualization of near-infrared laser beams in the research lab. The resulting ZIF-8–PMMA composite is exposed to a laser under extreme conditions and exhibits enhanced operating limits, much higher than that of the widely used inorganic materials in optics. Overall, our findings support the utilization of MOFs for synthesis of functional composites for optical application.
Characteristics of cortical spreading depression and c-Fos expression in transgenic mice having a mutation associated with familial hemiplegic migraine 2

Background Cortical spreading depression is thought to be the underlying mechanism of migraine aura. In 2006, three relatives having the point mutation E700K in ATP1A2 exon 15 were diagnosed with familial hemiplegic migraine 2 characterized by complicated forms of aura. Here, we generated a transgenic mouse model having the human E700K mutation in the Atp1a2 orthologous gene. Objective To investigate the characteristics of cortical spreading depression in a mouse model with E700K mutation in the Atp1a2. Methods Cortical spreading depression was induced by applying stepwise increases of KCl concentration or electrical stimulation intensity to C57BL/6J-Tg(Atp1a2*E700K)9151Kwk mice (Tg, both sexes) and corresponding wild-type animals. Under urethane anesthesia, the responsiveness and threshold to cortical spreading depression were examined and the distribution of c-Fos expression, a neuronal activity marker, was immunohistochemically determined. Results Overall, Tg mice showed significantly faster propagation velocity (p < 0.01) and longer full-width-at-half-maximum (p < 0.01) than wild-type animals, representing a slower recovery from direct current potential deflection. The cortical spreading depression threshold tended to be lower in Tg, especially in females. c-Fos-positive cells were significantly enhanced in the ipsilateral somatosensory cortex, piriform cortex, amygdala and striatum (each p < 0.05 vs. contralateral side). Numbers of c-Fos positive cells were significantly higher in the ipsilateral amygdala of Tg, as compared with wild-type animals (p < 0.01). Conclusion The effect of cortical spreading depression may be greater in E700K transgenic mice than that in wild-type animals, while the threshold for cortical spreading depression shows little change. Higher c-Fos expression in the amygdala may indicate alterations of the limbic system in Tg, suggesting an enhanced linkage between cortical spreading depression and amygdala connectivity in familial hemiplegic migraine 2 patients.
Cell culture dimensionality influences mesenchymal stem cell fate through cadherin-2 and cadherin-11

The acquisition of a specific cell fate is one of the core aims of tissue engineering and regenerative medicine. Significant evidence shows that aggregate cultures have a positive influence on fate decisions, presumably through cell-cell interactions, but little is known about the specific mechanisms. To investigate the difference between cells cultured as a monolayer and as aggregates, we started by looking at cadherin expression, an important protein involved in cell adhesion, during the differentiation of bone marrow-derived human mesenchymal stem cells (hMSCs) in aggregate and monolayer cultures. We observed that proliferating hMSCs in monolayer culture express cadherin-2 and undergo a switch to cadherin-11 over time, which was not evident in the aggregate cultures. By knocking down cadherin-2 and cadherin-11, we found that both cadherins were required for adipogenic differentiation in a monolayer as well as aggregate culture. However, during osteogenic differentiation, low levels of cadherin-2 were found to be favorable for cells cultured as a monolayer and as aggregates, whereas cadherin-11 was dispensable for cells cultured as aggregates. Together, these results provide compelling evidence for the important role that cadherins play in regulating the differentiation of hMSCs and how this is affected by the dimensionality of cell culture.