Development of a Rapid Epstein-Barr Virus Detection System Based on Recombinase Polymerase Amplification and a Lateral Flow Assay.

The quality of cellular products used in biological research can directly impact the ability to obtain accurate results. Epstein-Barr virus (EBV) is a latent virus that spreads extensively worldwide, and cell lines used in experiments may carry EBV and pose an infection risk. The presence of EBV in a single cell line can contaminate other cell lines used in the same laboratory, affecting experimental results. We developed three EBV detection systems: (1) a polymerase chain reaction (PCR)-based detection system, (2) a recombinase polymerase amplification (RPA)-based detection system, and (3) a combined RPA-lateral flow assay (LFA) detection system. The minimum EBV detection limits were 1 × 103 copy numbers for the RPA-based and RPA-LFA systems and 1 × 104 copy numbers for the PCR-based system. Both the PCR and RPA detection systems were applied to 192 cell lines, and the results were consistent with those obtained by the EBV assay methods specified in the pharmaceutical industry standards of the People's Republic of China. A total of 10 EBV-positive cell lines were identified. The combined RPA-LFA system is simple to operate, allowing for rapid result visualization. This system can be implemented in laboratories and cell banks as part of a daily quality control strategy to ensure cell quality and experimental safety and may represent a potential new technique for the rapid detection of EBV in clinical samples.

Investigation of the mixed origins of the MGC-803 cell line reveals that it is a hybrid cell line derived from HeLa.

Human cancer cell lines have an essential role in cancer research, but only authentic cell lines should be used as biological models. Authentication testing using short tandem repeat (STR) loci has shown that MGC-803 cells, which were reported to come from gastric adenocarcinoma, are similar to HeLa. In this study, we confirmed that the MGC-803 cell line contains genetic material from HeLa, including genetic sequence from human papilloma virus 18 (HPV18). Additional alleles were present on STR analysis that remained stable after extensive passaging and generation of mono-clones. This behavior is consistent with a hybrid cell line arising from cell-cell fusion. Further genetic analysis revealed that MGC-803 originated from donors with different genetic ancestries, one African (HeLa) and the other Asian. Transcriptomic analysis demonstrated that MGC-803 closely resembles HeLa and another nasopharyngeal-HeLa hybrid cell line CNE-2. Based on these findings, we conclude that MGC-803 is a hybrid cell line derived from HeLa and other cells, the latter derived from a different patient with Asian genetic ancestry.

A novel protocol to derive cervical motor neurons from induced pluripotent stem cells for amyotrophic lateral sclerosis.

Sporadic amyotrophic lateral sclerosis (sALS) is the majority of ALS, and the lack of appropriate disease models has hindered its research. Induced pluripotent stem cell (iPSC) technology now permits derivation of iPSCs from somatic cells of sALS patients to investigate disease phenotypes and mechanisms. Most existing differentiation protocols are time-consuming or low efficient in generating motor neurons (MNs). Here we report a rapid and simple protocol to differentiate MNs in monolayer culture using small molecules, which led to nearly pure neural stem cells in 6 days, robust OLIG2+ pMNs (73%-91%) in 12 days, enriched CHAT+ cervical spinal MNs (sMNs) (88%-97%) in 18 days, and functionally mature sMNs in 28 days. This simple and reproducible protocol permitted the identification of hyperexcitability phenotypes in our sALS iPSC-derived sMNs, and its application in neurodegenerative diseases should facilitate in vitro disease modeling, drug screening, and the development of cell therapy.

The putative protein kinase Stk36 is essential for ciliogenesis and CSF flow by associating with Ulk4.

Motile cilia lining on the ependymal cells are crucial for cerebrospinal fluid (CSF) flow and its dysfunction is often associated with hydrocephalus. Unc51-like-kinase 4 (Ulk4) was previously linked to CSF flow and motile ciliogenesis in mice, as the hypomorph mutant of Ulk4 (Ulk4tm1a/tm1a ) developed hydrocephalic phenotype resulted from defective ciliogenesis and disturbed ciliary motility, while the underling mechanism is largely obscure. Here, we report that serine/threonine kinase 36 (STK36), a paralog of ULK4, directly interacts with ULK4 and this was demonstrated by yeast two-hybrid (Y2H) in yeast and coimmunoprecipitation (co-IP) assays in HEK293T cells, respectively. The interaction region was confined to their respective N-terminal kinase domain. The hypomorph mutant of Stk36 (Stk36tmE4-/- ) also developed progressive hydrocephalus postnatally and dysfunctional CSF flow, with multiple defects of motile cilia, including reduced ciliary number, disorganized ciliary orientation, defected axonemal structure and inconsistent base body (BB) orientation. Stk36tmE4-/- also disturbed the expression of Foxj1 transcription factor and a range of other ciliogenesis-related genes. All these morphological changes, motile cilia defects and transcriptional dysregulation in the Stk36tmE4-/- are practically copied from that in Ulk4tm1a/tm1a mice. Taken together, we conclude that both Stk36 and Ulk4 are crucial for CSF flow, they cooperate by direct binding with their kinase domain to regulate the Foxj1 transcription factor pathways for ciliogenesis and cilia function, not limited to CSF flow. The underlying molecular mechanism probably conserved in evolution and could be extended to other metazoans.

BACH1 encourages ferroptosis by activating KDM4C-mediated COX2 demethylation after cerebral ischemia-reperfusion injury.

It has been confirmed that BTB domain and CNC homologue 1 (BACH1) are involved in ferroptosis-related diseases. However, the function of BACH1 in cerebral ischemia-reperfusion injury (CIRI)-induced ferroptosis remains to be largely unrevealed. First, analysis of differentially expressed genes in CIRI based on the GEO dataset GSE119121 revealed that BACH1 was upregulated in CIRI. BACH1 level was prominently increased in middle cerebral artery occlusion (MCAO)/reperfusion model and oxygen-glucose deprivation/reoxygenation cell model. Further, knock-down of BACH1 markedly reduced iron ion concentration, ROS production, 4-HNE and lipid peroxidation levels and facilitated GSH content, cell viability and protein levels of GPX4 and SLC7A11, while an pcDNA-KDM4C or pcDNA-COX2 combined with BACH1 siRNA could not enhance this effect. Mechanistically, BACH1 bound on the KDM4C promoter to transcriptionally activate its expression. Besides, KDM4C could occupy the promoter locus of the COX2 gene, promoting the COX2 expression by eliminating H3K9me3. Overexpression of KDM4C or COX2 overturned the effects of BACH1 inhibition. In vivo findings displayed that brain infraction, pathological damage and neuronal loss rate in MCAO mice were conspicuously decreased after BACH1 knock-down. This study reveals that BACH1 encourages ferroptosis in neuroblastoma cells and CIRI mouse brain tissues by activating KDM4C-mediated COX2 demethylation.

Identification of Hub Genes and Potential Molecular Pathogenesis in Substantia Nigra in Parkinson's Disease via Bioinformatics Analysis.

Parkinson's disease (PD) is the second most common neurodegenerative disease, with significant socioeconomic burdens. One of the crucial pathological features of PD is the loss of dopaminergic neurons in the substantia nigra (SN). However, the exact pathogenesis remains unknown. Moreover, therapies to prevent neurodegenerative progress are still being explored. We performed bioinformatics analysis to identify candidate genes and molecular pathogenesis in the SN of patients with PD. We analyzed the expression profiles, GSE49036 and GSE7621, which included 31 SN tissues in PD samples and 17 SN tissues in healthy control samples, and identified 86 common differentially expressed genes (DEGs). Then, GO and KEGG pathway analyses of the identified DEGs were performed to understand the biological processes and significant pathways of PD. Subsequently, a protein-protein interaction network was established, with 15 hub genes and four key modules which were screened in this network. The expression profiles, GSE8397 and GSE42966, were used to verify these hub genes. We demonstrated a decrease in the expression levels of 14 hub genes in the SN tissues of PD samples. Our results indicated that, among the 14 hub genes, DRD2, SLC18A2, and SLC6A3 may participate in the pathogenesis of PD by influencing the function of the dopaminergic synapse. CACNA1E, KCNJ6, and KCNB1 may affect the function of the dopaminergic synapse by regulating ion transmembrane transport. Moreover, we identified eight microRNAs (miRNAs) that can regulate the hub genes and 339 transcription factors (TFs) targeting these hub genes and miRNAs. Subsequently, we established an mTF-miRNA-gene-gTF regulatory network. Together, the identification of DEGs, hub genes, miRNAs, and TFs could provide better insights into the pathogenesis of PD and contribute to the diagnosis and therapies.

A Pilot Study of Plantar Mechanics Distributions and Fatigue Profiles after Running on a Treadmill: Using a Support Vector Machine Algorithm.

The treadmill is widely used in running fatigue experiments, and the variation of plantar mechanical parameters caused by fatigue and gender, as well as the prediction of fatigue curves by a machine learning algorithm, play an important role in providing different training programs. This experiment aimed to compare changes in peak pressure (PP), peak force (PF), plantar impulse (PI), and gender differences of novice runners after they were fatigued by running. A support vector machine (SVM) was used to predict the fatigue curve according to the changes in PP, PF, and PI before and after fatigue. 15 healthy males and 15 healthy females completed two runs at a speed of 3.3 m/s ± 5% on a footscan pressure plate before and after fatigue. After fatigue, PP, PF, and PI decreased at hallux (T1) and second-fifth toes (T2-5), while heel medial (HM) and heel lateral (HL) increased. In addition, PP and PI also increased at the first metatarsal (M1). PP, PF, and PI at T1 and T2-5 were significantly higher in females than in males, and metatarsal 3-5 (M3-5) were significantly lower in females than in males. The SVM classification algorithm results showed the accuracy was above average level using the T1 PP/HL PF (train accuracy: 65%; test accuracy: 75%), T1 PF/HL PF (train accuracy: 67.5%; test accuracy: 65%), and HL PF/T1 PI (train accuracy: 67.5%; test accuracy: 70%). These values could provide information about running and gender-related injuries, such as metatarsal stress fractures and hallux valgus. Application of the SVM to the identification of plantar mechanical features before and after fatigue. The features of the plantar zones after fatigue can be identified and the learned algorithm of plantar zone combinations with above-average accuracy (T1 PP/HL PF, T1 PF/HL PF, and HL PF/T1 PI) can be used to predict running fatigue and supervise training. It provided an important idea for the detection of fatigue after running.

Nasal mucosal care before and after nasal endoscopic surgery based on computational information system resource sharing technology.

This study presents an in-depth analysis on a machine-designed computational web-based information system, which was used to conduct nasal mucosal care before and after nasal endoscopic surgery for chronic sinusitis. The system was developed and implemented using the mainstream B/S structure model with a Java development framework and MySQL database. Sinus irrigation solution has been shown to be effective for postoperative flushing after nasal endoscopy, by eliminating mucosal edema and promoting mucosal epithelialization at the operative cavity, and it is currently a desirable method that deserves promotion. By comparing the time required for surgical cavity cleaning, the rinsing solution was shown to be key of the physical flushing effect in the initial period after nasal endoscopy. It could remove blood cemented and surgical cavity surface cemented skin and secretions. In addition, the sinus irrigation solution can accelerate the mucosal epithelialization of the operative cavity more effectively than compounded saline. It could effectively eliminate mucosal edema, restore its protective and defensive functions, and help local blood circulation, secretion absorption, mucosal growth, mucosal regeneration and repair, and mucus cilia removal.

A silver lining in cell line authentication: Short tandem repeat analysis of 1373 cases in China from 2010 to 2019.

Continuous cell lines are practical models that are widely used in the study of disease mechanisms and particularly cancers. However, the issue of cell line cross-contamination has existed since the 1960s, despite repeated advocation for cell line authentication by many experts. Furthermore, cell line abuse has been underestimated and underreported. The China Center for Type Culture Collection (CCTCC) received 1373 cell samples for authentication from 2010 to 2019, and has found that the quality of cell lines has improved during this time, offering a positive outlook for the future.

Arch-Support Induced Changes in Foot-Ankle Coordination in Young Males with Flatfoot during Unplanned Gait Termination.

OBJECTIVE: The efficacy of arch orthoses in posture adjustment and joint coordination improvement during steady-state gait is well documented; however, the biomechanical changes of gait sub-tasks caused by arch support (AS), especially during gait termination, are poorly understood. Hence, this study aimed to investigate how the acute arch-supporting intervention affects foot-ankle coordination and coordination variability (CV) in individuals with flatfoot during unplanned gait termination (UGT). METHODS: Twenty-five male patients with flatfoot were selected as subjects participated in this AS manipulation study. A motion capture system was used for the collection of the metatarsophalangeal joint (MPJ) and ankle kinematics during UGT. MPJ-Ankle coordination and CV were quantified using an optimized vector coding technique during the three sub-phases of UGT. A paired-sample t-test from the one-dimensional statistical parametric mapping of one-dimensional was applied to examine the data significance. RESULTS: Significant differences for the joint kinematics between non-arch-support (NAS) and AS were exhibited only in the MPJ transverse plane during the middle and later periods of UGT (p = 0.04-0.026). Frontal plane MPJ-ankle coordination under AS during stimulus delay significantly decreased from 177.16 ± 27.41° to 157.75 ± 32.54° compared with under NAS (p = 0.026); however, the coordination pattern had not changed. Moreover, no significant difference was found in the coupling angle variability between NAS and AS in three planes during sub-phases of UGT (all p > 0.5). CONCLUSIONS: The detailed intrinsic characteristic of AS induced acute changes in lower extremity segment coordination in patients with mild flatfoot has been recorded. This dataset on foot-ankle coordination characteristics during UGT is essential for explaining foot function and injury prediction concerning AS manipulation. Further studies are expected to reflect lower limb inter-joint coordination during gait termination through the long-term effects of AS orthoses.

Generation and characterization of three induced pluripotent stem cell lines (NUIGi046-A, NUIGi046-B, NUIGi046-C) from a 51-year-old healthy individual.

Skin punch biopsy was donated by a healthy 51-year-old Caucasian male and the dermal fibroblasts were reprogrammed into human induced pluripotent stem cell (hiPSC) lines by using non-integrative Sendai viruses expressing OCT4, SOX2, KLF4 and c-MYC. Three iPSC lines (NUIGi046-A, NUIGi046-B, NUIGi046-C) highly expressed the pluripotent markers and were capable of differentiating into cells of endodermal, mesodermal, and ectodermal origin. These iPSCs can be offered as controls and in combination with genome-editing and three-dimensional (3D) system. They may be used for human disease modelling and drug screening.

Derivation and characterization of two human induced pluripotent stem cell lines (NUIGi004-A) and (NUIGi012-A) from two patients with LQT2 disease.

Long QT syndrome type 2 (LQT2) is associated with KCNH2, which encodes the α subunit of the ion channel that controls the K+ current in the heart. Mutations of KCNH2 cause loss of Kv11.1 channel function by disrupting subunit folding, assembly, or trafficking of the channel to the cell surface. Here we generated two induced pluripotent stem cell (iPSC) lines from two patients carrying mutation in KCNH2 gene. These iPSCs express the pluripotent markers and have the capacity of differentiation into other cell types. These patient-derived iPSCs are useful for investigating the disease pathology and identifying the therapeutic target.

Derivation of four iPSC lines from a male ASD patient carrying a deletion in the middle coding region of NRXN1α gene (NUIGi039-A and NUIGi039-B) and a male sibling control (NUIGi040-A and NUIGi040-B).

NRXN1 deletions are commonly found in autism spectrum disorder (ASD) and other neurodevelopmental/neuropsychiatric disorders. Derivation of induced pluripotent stem cells (iPSCs) from different diseases involving different deletion regions are essential, as NRXN1 may produce thousands of splicing variants. We report here the derivation of iPSCs from a sibling control and an ASD proband carrying de novo heterozygous deletions in the middle region of NRXN1, using a non-integrating Sendai viral kit. The genotype and karyotype of the iPSCs were validated by whole genome SNP array. All iPSC lines highly expressed pluripotency markers and could be differentiated into three germ layers.

Derivation of iPSC lines from two patients with autism spectrum disorder carrying NRXN1α deletion (NUIGi041-A, NUIG041-B; NUIGi045-A) and one sibling control (NUIGi042-A, NUIGi042-B).

NRXN1 encodes thousands of splicing variants categorized into long NRXN1α, short NRXN1ß and extremely short NRXN1γ, which exert differential roles in neuronal excitation/inhibition. NRXN1α deletions are common in autism spectrum disorder (ASD) and other neurodevelopmental/neuropsychiatric disorders. We derived induced pluripotent stem cells (iPSCs) from one sibling control and two ASD probands carrying NRXN1α+/-, using non-integrating Sendai viral method. All iPSCs highly expressed pluripotency markers and could be differentiated into ectodermal/mesodermal/endodermal cells. The genotype and karyotype of the iPSCs were validated by whole genome SNP array. The availability of the iPSCs offers an opportunity for understanding NRXN1α function in human neurons and in ASD.

Advantages of a 21-loci short tandem repeat method for detection of cross-contamination in human cell lines.

Cross-contamination of cell lines is a highly relevant and pervasive problem. The analysis of short tandem repeats (STR) is a simple and commercially available technique to authenticate cell lines for more than two decades. At present, STR multiple amplification kits have been developed up to 21 loci while the current STR databases only provide 9-loci STR profiles. Here, we compared the advantages of 21-loci STR methodology using the same algorithm as 9-loci method. The 21-loci method reduced the uncertainty ratio for authentications by 97.5% relative to the 9-loci method and exclude effectively false positive. We show that the additional 12 loci helped to greatly reduce sample-site marker specificity arising from genetic isolation and the occurrence of null alleles, suggesting that inclusion of additional loci in these databases will ultimately improve the efficiency and accuracy of authentication of cell lines. Taken together, we demonstrate the utility of a 21-loci method in human cells, providing a novel marker panel for use as a valuable alternative to 9-loci analyses to minimize cell line authentication errors and reduce costs due to erroneous experiments.

Generation of twelve induced pluripotent stem cell lines from two healthy controls and two patients with sporadic amyotrophic lateral sclerosis.

The majority of amyotrophic lateral sclerosis are sporadic (sALS) with no familial history or known genetic association, therefore a large cohort of disease models are required to identify common mechanisms or to test therapeutic interventions. Here we generated twelve induced pluripotent stem cell (iPSC) lines from human dermal fibroblasts of two healthy individuals and two sALS patients lacking common ALS mutations, using non-integrational Sendai virus expressing reprogramming factors OCT3/4, KLF4, SOX2 and c-MYC. The iPSC lines highly expressed pluripotency markers could be spontaneously differentiated into three embryonic germ layers, with no gross chromosomal aberrations or specific copy number variations.

Agonist-specific voltage-dependent gating of lysosomal two-pore Na+ channels.

Mammalian two-pore-channels (TPC1, 2; TPCN1, TPCN2) are ubiquitously- expressed, PI(3,5)P2-activated, Na+-selective channels in the endosomes and lysosomes that regulate luminal pH homeostasis, membrane trafficking, and Ebola viral infection. Whereas the channel activity of TPC1 is strongly dependent on membrane voltage, TPC2 lacks such voltage dependence despite the presence of the presumed 'S4 voltage-sensing' domains. By performing high-throughput screening followed by lysosomal electrophysiology, here we identified a class of tricyclic anti-depressants (TCAs) as small-molecule agonists of TPC channels. TCAs activate both TPC1 and TPC2 in a voltage-dependent manner, referred to as Lysosomal Na+ channel Voltage-dependent Activators (LyNa-VAs). We also identified another compound which, like PI(3,5)P2, activates TPC2 independent of voltage, suggesting the existence of agonist-specific gating mechanisms. Our identification of small-molecule TPC agonists should facilitate the studies of the cell biological roles of TPCs and can also readily explain the reported effects of TCAs in the modulation of autophagy and lysosomal functions.

Generation of six induced pluripotent stem cell (iPSC) lines from two patients with amyotrophic lateral sclerosis (NUIGi043-A, NUIGi043-B, NUIGi043-C, NUIGi044-A, NUIGi044-B, NUIGi044-C).

In this study, we generated 6 induced pluripotent stem cell (iPSC) lines derived from dermal fibroblasts of patients with sporadic amyotrophic lateral sclerosis (sALS). The fibroblasts were reprogrammed using non-integrating Sendai viruses containing four reprogramming factors OCT3/4, SOX2, KLF4 and C-MYC. The iPSC lines displayed normal molecular karyotype, expressed pluripotency markers and were capable of differentiating into three embryonic germ layers.

Rapamycin directly activates lysosomal mucolipin TRP channels independent of mTOR.

Rapamycin (Rap) and its derivatives, called rapalogs, are being explored in clinical trials targeting cancer and neurodegeneration. The underlying mechanisms of Rap actions, however, are not well understood. Mechanistic target of rapamycin (mTOR), a lysosome-localized protein kinase that acts as a critical regulator of cellular growth, is believed to mediate most Rap actions. Here, we identified mucolipin 1 (transient receptor potential channel mucolipin 1 [TRPML1], also known as MCOLN1), the principle Ca2+ release channel in the lysosome, as another direct target of Rap. Patch-clamping of isolated lysosomal membranes showed that micromolar concentrations of Rap and some rapalogs activated lysosomal TRPML1 directly and specifically. Pharmacological inhibition or genetic inactivation of mTOR failed to mimic the Rap effect. In vitro binding assays revealed that Rap bound directly to purified TRPML1 proteins with a micromolar affinity. In both healthy and disease human fibroblasts, Rap and rapalogs induced autophagic flux via nuclear translocation of transcription factor EB (TFEB). However, such effects were abolished in TRPML1-deficient cells or by TRPML1 inhibitors. Hence, Rap and rapalogs promote autophagy via a TRPML1-dependent mechanism. Given the demonstrated roles of TRPML1 and TFEB in cellular clearance, we propose that lysosomal TRPML1 may contribute a significant portion to the in vivo neuroprotective and anti-aging effects of Rap via an augmentation of autophagy and lysosomal biogenesis.