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1.
Nat Commun ; 14(1): 3363, 2023 06 08.
Article in English | MEDLINE | ID: mdl-37291154

ABSTRACT

Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.


Subject(s)
Genome, Mitochondrial , Rhodophyta , Phylogeny , Genome, Mitochondrial/genetics , Eukaryotic Cells , Mitochondria/genetics , Rhodophyta/genetics , Evolution, Molecular
2.
Transp Res D Transp Environ ; 120: 103753, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37292493

ABSTRACT

This study aims a more thorough understanding of individuals' motivations and determinants of working from home (WFH) at various phases of the pandemic. To achieve this research goal, we analyze attitudes towards WFH, the profiles of various types of workers engaged in WFH, and the determinants of the current and future expected frequency of WFH among 816 workers in Hong Kong. We identify four types of teleworkers: (1) those with little employer support, (2) those distracted with tech problems, (3) those with good home office, and (4) those with substantial employer support. Separate latent-class choice models present that WFH frequencies in early phases of the pandemic (and at the moment), attitudes towards WFH, and certain constraining/facilitating factors affect the (expected) frequency of WFH. This study provides valuable insights into the types of teleworkers and the determinants of WFH, which will help policymakers create ways to encourage (or discourage) the future frequency of WFH.

3.
Transp Res Rec ; 2677(4): 298-312, 2023 Apr.
Article in English | MEDLINE | ID: mdl-37153190

ABSTRACT

The COVID-19 pandemic has caused a huge disruption worldwide with direct and indirect effects on travel behavior. In response to extensive community spread and potential risk of infection, during the early stage of the pandemic many state and local governments implemented non-pharmaceutical interventions that restricted non-essential travel for residents. This study evaluates the impacts of the pandemic on mobility by analyzing micro panel data (N = 1,274) collected in the United States via online surveys in two periods, before and during the early phase of the pandemic. The panel makes it possible to observe initial trends in travel behavior change, adoption of online shopping, active travel, and use of shared mobility services. This analysis intends to document a high-level overview of the initial impacts to spur future research to dive deeper into these topics. With the analysis of the panel data, substantial shifts are found from physical commutes to teleworking, more adoption of e-shopping and home delivery services, more frequent trips by walking and biking for leisure purposes, and changes in ridehailing use with substantial variations across socioeconomic groups. The social and environmental implications of these findings are discussed and suggestions for effective policy and directions for future research are made in the conclusion.

4.
Front Public Health ; 11: 1128889, 2023.
Article in English | MEDLINE | ID: mdl-37089495

ABSTRACT

Introduction: This study sets out to provide scientific evidence on the spatial risk for the formation of a superspreading environment. Methods: Focusing on six common types of urban facilities (bars, cinemas, gyms and fitness centers, places of worship, public libraries and shopping malls), it first tests whether visitors' mobility characteristics differ systematically for different types of facility and at different locations. The study collects detailed human mobility and other locational data in Chicago, Hong Kong, London, São Paulo, Seoul and Zurich. Then, considering facility agglomeration, visitors' profile and the density of the population, facilities are classified into four potential spatial risk (PSR) classes. Finally, a kernel density function is employed to derive the risk surface in each city based on the spatial risk class and nature of activities. Results: Results of the human mobility analysis reflect the geographical and cultural context of various facilities, transport characteristics and people's lifestyle across cities. Consistent across the six global cities, geographical agglomeration is a risk factor for bars. For other urban facilities, the lack of agglomeration is a risk factor. Based on the spatial risk maps, some high-risk areas of superspreading are identified and discussed in each city. Discussion: Integrating activity-travel patterns in risk models can help identify areas that attract highly mobile visitors and are conducive to superspreading. Based on the findings, this study proposes a place-based strategy of non-pharmaceutical interventions that balance the control of the pandemic and the daily life of the urban population.


Subject(s)
Urban Population , Humans , Cities , Brazil , Hong Kong , Seoul
5.
Nat Commun ; 14(1): 10, 2023 01 04.
Article in English | MEDLINE | ID: mdl-36599855

ABSTRACT

The high temperature, acidity, and heavy metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived in hot springs and associated sites worldwide for more than 1 billion years. Here, we analyze chromosome-level assemblies from three representative Cyanidiophyceae species to study environmental adaptation at the genomic level. We find that subtelomeric gene duplication of functional genes and loss of canonical eukaryotic traits played a major role in environmental adaptation, in addition to horizontal gene transfer events. Shared responses to environmental stress exist in Cyanidiales and Galdieriales, however, most of the adaptive genes (e.g., for arsenic detoxification) evolved independently in these lineages. Our results underline the power of local selection to shape eukaryotic genomes that may face vastly different stresses in adjacent, extreme microhabitats.


Subject(s)
Hot Springs , Metals, Heavy , Rhodophyta , Rhodophyta/genetics , Genome/genetics , Acclimatization , Phylogeny
6.
Immune Netw ; 18(1): e5, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29503738

ABSTRACT

Chemokine (C-X3-C motif) ligand 1 (CX3CL1, also known as fractalkine) and its receptor chemokine (C-X3-C motif) receptor 1 (CX3CR1) are widely expressed in immune cells and non-immune cells throughout organisms. However, their expression is mostly cell type-specific in each tissue. CX3CR1 expression can be found in monocytes, macrophages, dendritic cells, T cells, and natural killer (NK) cells. Interaction between CX3CL1 and CX3CR1 can mediate chemotaxis of immune cells according to concentration gradient of ligands. CX3CR1 expressing immune cells have a main role in either pro-inflammatory or anti-inflammatory response depending on environmental condition. In a given tissue such as bone marrow, brain, lung, liver, gut, and cancer, CX3CR1 expressing cells can maintain tissue homeostasis. Under pathologic conditions, however, CX3CR1 expressing cells can play a critical role in disease pathogenesis. Here, we discuss recent progresses of CX3CL1/CX3CR1 in major tissues and their relationships with human diseases.

7.
Microb Pathog ; 96: 10-4, 2016 Jul.
Article in English | MEDLINE | ID: mdl-27133265

ABSTRACT

To investigate the expression patterns of chitinase on SDS-PAGE gel, Paenibacillus ehimensis MA2012 was incubated in gelatin-chitin medium (GCM) at 30 °C for 7 days. Six major bands (Ch3, Ch4, Ch5, Ch6, Ch7, and Ch8) of chitinase isozymes in GC medium appeared on SDS-PAGE gel during the incubation period. Chitinase activity staining of P. ehimensis MA2012 was detected on 2-DE with different pI values (4-11). After DEAE-Sephadex chromatography, eight bands (Ch1 to Ch8) of chitinase isozymes were stained strongly with Calcofluor white M2R at fraction 45. After Sephadex G-75 gel filtration, six bands (Ch3 to Ch8) of chitinase isozymes were stained with Calcofluor white M2R at fractions of 11-12. The specific activity of the purified chitinase was 3.8 units mg(-1) protein with a purification factor of 0.27. Inhibition rate of the conidial germination of Colletotrichum gloeosporioides was 87% in partial purified chitinase treatment compared with control.


Subject(s)
Antifungal Agents/metabolism , Chitinases/metabolism , Colletotrichum/drug effects , Paenibacillus/enzymology , Spores, Fungal/drug effects , Antifungal Agents/isolation & purification , Chitinases/isolation & purification , Chromatography, Gel , Chromatography, Ion Exchange , Culture Media/chemistry , Electrophoresis, Gel, Two-Dimensional , Electrophoresis, Polyacrylamide Gel , Gene Expression Profiling , Isoenzymes/isolation & purification , Isoenzymes/metabolism , Paenibacillus/growth & development , Temperature
8.
Clin Psychopharmacol Neurosci ; 14(1): 26-32, 2016 Feb 29.
Article in English | MEDLINE | ID: mdl-26792037

ABSTRACT

OBJECTIVE: Cognitive symptoms are an important component of depression and the Perceived Deficits Questionnaire-Depression is one of only a few instruments available for the subjective assessment of cognitive dysfunction in depression. Thus, the present study aimed to validate a Korean version of the PDQ-D (K-PDQ-D) using patients with major depressive disorder (MDD). METHODS: This study included 128 MDD patients who were assessed at study entry and 86 of these patients were then completed 12 weeks of antidepressant monotherapy. All subjects were assessed with the K-PDQ-D, the Montgomery-Asberg Depression Rating Scale (MADRS), the Sheehan Disability Scale (SDS), the EuroQol-5 dimensions questionnaire (EQ-5D), and the number of sick leave days taken in the previous week. The internal consistency, Guttman's split-half and test-retest reliabilities, factorial analyses, and concurrent and predictive validities of the K-PDQ-D were investigated. RESULTS: The K-PDQ-D exhibited excellent internal consistency and reliabilities, and was composed of four factors with high coefficients of determination. The concurrent validity analyses revealed that the K-PDQ-D scores were significantly correlated with the MADRS, SDS, and EQ-5D scores and the number of sick leave days taken. The K-PDQ-D scores at study entry significantly predicted changes in sick leave days and EQ-5D score from study entry to the 12-week endpoint. CONCLUSION: The newly developed K-PDQ-D is a reliable and valid instrument for the evaluation of subjective cognitive symptoms in MDD patients. The K-PDQ-D may assist in the gathering of unique information regarding subjective cognitive complaints, which is important for the comprehensive evaluation of patients with MDD.

9.
J Biol Chem ; 290(28): 17401-14, 2015 Jul 10.
Article in English | MEDLINE | ID: mdl-26023233

ABSTRACT

Recent groundbreaking work has demonstrated that combined expression of the transcription factors Brn2, Ascl1, and Myt1L (BAM; also known as Wernig factors) convert mouse fibroblasts into postmitotic neuronal cells. However, questions remain regarding whether trans-conversion is achieved directly or involves an intermediary precursor stage. Trans-conversion toward expandable neural precursor cells (NPCs) is more useful than direct one-step neuron formation with respect to yielding a sufficient number of cells and the feasibility of manipulating NPC differentiation toward certain neuron subtypes. Here, we show that co-expression of Wernig factors and Bcl-xL induces fibroblast conversion into NPCs (induced NPCs (iNPCs)) that are highly expandable for >100 passages. Gene expression analyses showed that the iNPCs exhibited high expression of common NPC genes but not genes specific to defined embryonic brain regions. This finding indicated that a regional identity of iNPCs was not established. Upon induction, iNPCs predominantly differentiated into astrocytes. However, the differentiation potential was not fixed and could be efficiently manipulated into general or specific subtypes of neurons by expression of additional genes. Specifically, overexpression of Nurr1 and Foxa2, transcription factors specific for midbrain dopamine neuron development, drove iNPCs to yield mature midbrain dopamine neurons equipped with presynaptic DA neuronal functions. We further assessed the therapeutic potential of iNPCs in Parkinson disease model rats.


Subject(s)
Cell Transdifferentiation , Dopamine/metabolism , Dopaminergic Neurons/cytology , Dopaminergic Neurons/metabolism , Fibroblasts/cytology , Fibroblasts/metabolism , Neural Stem Cells/cytology , Neural Stem Cells/metabolism , Animals , Basic Helix-Loop-Helix Transcription Factors/genetics , Cellular Reprogramming , Gene Expression , Hepatocyte Nuclear Factor 3-beta/genetics , Mesencephalon/cytology , Mesencephalon/metabolism , Mice , Mice, Inbred C57BL , Mice, Inbred ICR , Mice, Transgenic , Nerve Tissue Proteins/genetics , Nuclear Receptor Subfamily 4, Group A, Member 2/genetics , POU Domain Factors/genetics , Parkinsonian Disorders/metabolism , Parkinsonian Disorders/pathology , Parkinsonian Disorders/therapy , Rats , Rats, Inbred Lew , Rats, Wistar , Transcription Factors/genetics
10.
Stem Cells ; 29(11): 1861-73, 2011 Nov.
Article in English | MEDLINE | ID: mdl-21922608

ABSTRACT

Understanding midbrain dopamine (DA) neuron differentiation is of importance, because of physiological and clinical implications of this neuronal subtype. We show that prolonged membrane depolarization induced by KCl treatment promotes DA neuron differentiation from neural precursor cells (NPCs) derived from embryonic ventral midbrain (VM). Interestingly, the depolarization-induced increase of DA neuron yields was not abolished by L-type calcium channel blockers, along with no depolarization-mediated change of intracellular calcium level in the VM-derived NPCs (VM-NPCs), suggesting that the depolarization effect is due to a calcium-independent mechanism. Experiments with labeled DA neuron progenitors indicate that membrane depolarization acts at the differentiation fate determination stage and promotes the expression of DA phenotype genes (tyrosine hydroxylase [TH] and DA transporter [DAT]). Recruitment of Nurr1, a transcription factor crucial for midbrain DA neuron development, to the promoter of TH gene was enhanced by depolarization, along with increases of histone 3 acetylation (H3Ac) and trimethylation of histone3 on lysine 4 (H3K4m3), and decreases of H3K9m3 and H3K27m3 in the consensus Nurr1 binding regions of TH promoter. Depolarization stimuli on differentiating VM-NPCs also induced dissociation of methyl CpG binding protein 2 and related repressor complex molecules (repressor element-1 silencing transcription factor corepressor and histone deacetylase 1) from the CpG sites of TH and DAT promoters. Based on these findings, we suggest that membrane depolarization promotes DA neuron differentiation by opening chromatin structures surrounding DA phenotype genes and inhibiting the binding of corepressors, thus allowing transcriptional activators such as Nurr1 to access DA neuron differentiation gene promoter regions.


Subject(s)
Cell Differentiation/physiology , Dopaminergic Neurons/cytology , Dopaminergic Neurons/metabolism , Histones/metabolism , Mesencephalon/cytology , Neural Stem Cells/cytology , Neural Stem Cells/metabolism , Animals , Calcium/metabolism , Cell Differentiation/genetics , Cell Proliferation , Cell Survival/genetics , Cell Survival/physiology , Cells, Cultured , DNA Methylation/genetics , Epigenesis, Genetic/genetics , Histones/genetics , Immunohistochemistry , Methyl-CpG-Binding Protein 2/genetics , Nuclear Receptor Subfamily 4, Group A, Member 2/genetics , Rats , Real-Time Polymerase Chain Reaction
11.
J Clin Invest ; 121(6): 2326-35, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21576821

ABSTRACT

Parkinson disease (PD) involves the selective loss of midbrain dopamine (mDA) neurons and is a possible target disease for stem cell-based therapy. Human induced pluripotent stem cells (hiPSCs) are a potentially unlimited source of patient-specific cells for transplantation. However, it is critical to evaluate the safety of hiPSCs generated by different reprogramming methods. Here, we compared multiple hiPSC lines derived by virus- and protein-based reprogramming to human ES cells (hESCs). Neuronal precursor cells (NPCs) and dopamine (DA) neurons delivered from lentivirus-based hiPSCs exhibited residual expression of exogenous reprogramming genes, but those cells derived from retrovirus- and protein-based hiPSCs did not. Furthermore, NPCs derived from virus-based hiPSCs exhibited early senescence and apoptotic cell death during passaging, which was preceded by abrupt induction of p53. In contrast, NPCs derived from hESCs and protein-based hiPSCs were highly expandable without senescence. DA neurons derived from protein-based hiPSCs exhibited gene expression, physiological, and electrophysiological properties similar to those of mDA neurons. Transplantation of these cells into rats with striatal lesions, a model of PD, significantly rescued motor deficits. These data support the clinical potential of protein-based hiPSCs for personalized cell therapy of PD.


Subject(s)
Cellular Reprogramming , Dopamine/metabolism , Induced Pluripotent Stem Cells/physiology , Kruppel-Like Transcription Factors/physiology , Neurons/cytology , Octamer Transcription Factor-3/physiology , Parkinsonian Disorders/surgery , Proto-Oncogene Proteins c-myc/physiology , SOXB1 Transcription Factors/physiology , Animals , Apoptosis , Arginine , Cell Differentiation , Cell Line/transplantation , Cell Lineage , Cellular Senescence , Gene Expression Regulation, Developmental , Genes, p53 , Genetic Vectors/pharmacology , Humans , Induced Pluripotent Stem Cells/transplantation , Kruppel-Like Factor 4 , Kruppel-Like Transcription Factors/genetics , Lentivirus/physiology , Neurons/metabolism , Octamer Transcription Factor-3/genetics , Proto-Oncogene Proteins c-myc/genetics , Rats , Retroviridae/physiology , SOXB1 Transcription Factors/genetics , Tumor Suppressor Protein p53/biosynthesis
12.
Stem Cells ; 28(3): 501-12, 2010 Mar 31.
Article in English | MEDLINE | ID: mdl-20049900

ABSTRACT

Effective dopamine (DA) neuron differentiation from neural precursor cells (NPCs) is prerequisite for precursor/stem cell-based therapy of Parkinson's disease (PD). Nurr1, an orphan nuclear receptor, has been reported as a transcription factor that can drive DA neuron differentiation from non-dopaminergic NPCs in vitro. However, Nurr1 alone neither induces full neuronal maturation nor expression of proteins found specifically in midbrain DA neurons. In addition, Nurr1 expression is inefficient in inducing DA phenotype expression in NPCs derived from certain species such as mouse and human. We show here that Foxa2, a forkhead transcription factor whose role in midbrain DA neuron development was recently revealed, synergistically cooperates with Nurr1 to induce DA phenotype acquisition, midbrain-specific gene expression, and neuronal maturation. Thus, the combinatorial expression of Nurr1 and Foxa2 in NPCs efficiently yielded fully differentiated nigral (A9)-type midbrain neurons with clearly detectable DA neuronal activities. The effects of Foxa2 in DA neuron generation were observed regardless of the brain regions or species from which NPCs were derived. Furthermore, DA neurons generated by ectopic Foxa2 expression were more resistant to toxins. Importantly, Foxa2 expression resulted in a rapid cell cycle exit and reduced cell proliferation. Consistently, transplantation of NPCs transduced with Nurr1 and Foxa2 generated grafts enriched with midbrain-type DA neurons but reduced number of proliferating cells, and significantly reversed motor deficits in a rat PD model. Our findings can be applied to ongoing attempts to develop an efficient and safe precursor/stem cell-based therapy for PD.


Subject(s)
Cell Differentiation/genetics , Hepatocyte Nuclear Factor 3-beta/genetics , Neurons/metabolism , Nuclear Receptor Subfamily 4, Group A, Member 2/genetics , Stem Cell Transplantation/methods , Stem Cells/metabolism , Animals , Cell Proliferation , Cell Survival/genetics , Cell- and Tissue-Based Therapy/methods , Cells, Cultured , Dopamine/metabolism , Humans , Mice , Neurogenesis/genetics , Neurons/cytology , Neurons/transplantation , Parkinson Disease/surgery , Phenotype , Rats , Rats, Sprague-Dawley , Stem Cells/cytology , Substantia Nigra/cytology , Substantia Nigra/metabolism , Transfection/methods , Treatment Outcome
13.
Mol Ther ; 17(10): 1761-70, 2009 Oct.
Article in English | MEDLINE | ID: mdl-19603007

ABSTRACT

We have previously demonstrated derivation of neural precursor (NP) cells of a midbrain-type from human embryonic stem (hES) cells to yield an enriched population of dopamine (DA) neurons. These hES-derived NPs can be expanded in vitro through multiple passages without altering their DA neurogenic potential. Here, we studied two aspects of these hES-NP cells that are critical issues in cell therapeutic approaches for Parkinson's disease (PD): cell survival and tumorigenic potential. Neuroepithelial rosettes, a potentially tumorigenic structure, disappeared during hES-NP cell expansion in vitro. Although a minor population of cells positive for Oct3/4, a marker specific for undifferentiated hES cells, persisted in culture during hES-NP cell expansion, they could be completely eliminated by subculturing hES-NPs under differentiation-inducing conditions. Consistently, no tumors/teratomas are formed in rats grafted with multipassaged hES-NPs. However, extensively expanded hES-NP cells easily underwent cell death during differentiation in vitro and after transplantation in vivo. Transgenic expression of Bcl-XL and sonic hedgehog (SHH) completely overcame the cell survival problems without increasing tumor formation. These findings indicate that hES-NP cell expansion in conjunction with Bcl-XL+SHH transgene expression may provide a renewable and safe source of DA neurons for transplantation in PD.


Subject(s)
Dopamine/metabolism , Embryonic Stem Cells/cytology , Neurons/cytology , Animals , Apoptosis/drug effects , Brain-Derived Neurotrophic Factor/pharmacology , Cell Differentiation/drug effects , Cell Survival/drug effects , Cyclic AMP/pharmacology , Embryonic Stem Cells/drug effects , Female , Genetic Vectors/genetics , Glial Cell Line-Derived Neurotrophic Factor/pharmacology , Hedgehog Proteins/genetics , Hedgehog Proteins/physiology , Humans , Immunohistochemistry , Neurons/drug effects , Polymerase Chain Reaction , Rats , Rats, Sprague-Dawley , Retroviridae/genetics , bcl-X Protein/genetics , bcl-X Protein/physiology
14.
Stem Cells ; 27(9): 2238-46, 2009 Sep.
Article in English | MEDLINE | ID: mdl-19522012

ABSTRACT

Nurr1 is a transcription factor specific for the development and maintenance of the midbrain dopamine (DA) neurons. Exogenous Nurr1 in neural precursor (NP) cells induces the differentiation of DA neurons in vitro that are capable of reversing motor dysfunctions in a rodent model for Parkinson disease. The promise of this therapeutic approach, however, is unclear due to poor cell survival and phenotype loss of DA cells after transplantation. We herein demonstrate that Nurr1 proteins undergo ubiquitin-proteasome-system-mediated degradation in differentiating NP cells. The degradation process is activated by a direct Akt-mediated phosphorylation of Nurr1 proteins and can be prevented by abolishing the Akt-target sequence in Nurr1 (Nurr1(Akt)). Overexpression of Nurr1(Akt) in NP cells yielded DA neurons in which Nurr1 protein levels were maintained for prolonged periods. The sustained Nurr1 expression endowed the Nurr1(Akt)-induced DA neurons with resistance to toxic stimuli, enhanced survival, and sustained DA phenotypes in vitro and in vivo after transplantation.


Subject(s)
Dopamine/metabolism , Neurons/cytology , Neurons/metabolism , Nuclear Receptor Subfamily 4, Group A, Member 2/physiology , Animals , Basic Helix-Loop-Helix Transcription Factors/pharmacology , Blotting, Western , Butadienes/pharmacology , Calcium-Calmodulin-Dependent Protein Kinases/antagonists & inhibitors , Calcium-Calmodulin-Dependent Protein Kinases/physiology , Cell Differentiation/genetics , Cell Differentiation/physiology , Cell Line , Cell Survival/genetics , Cell Survival/physiology , Chromones/pharmacology , Enzyme Inhibitors/pharmacology , Flavonoids/pharmacology , Humans , Immunoprecipitation , Mesencephalon/cytology , Morpholines/pharmacology , Nitriles/pharmacology , Nuclear Receptor Subfamily 4, Group A, Member 2/genetics , Phosphatidylinositol 3-Kinases/physiology , Phosphoinositide-3 Kinase Inhibitors , Protein Stability/drug effects , Rats , Rats, Sprague-Dawley , Reverse Transcriptase Polymerase Chain Reaction
15.
Neurochem Res ; 34(6): 1030-8, 2009 Jun.
Article in English | MEDLINE | ID: mdl-18987971

ABSTRACT

A large amount of genetic information is devoted to brain development. In this study, the cortical development in rats at eight developmental time points (four embryonic [E15, E16, E18, E20] and four postnatal [P0, P7, P14, P21]) was studied using a rat brain 10K cDNA microarray. Significant differential expression was observed in 467 of the 9,805 genes represented on the microarray. Two major Gene Ontology classes-cell differentiation and cell-cell signaling-were found to be important for cortical development. Genes for ribosomal proteins, heterogeneous nuclear ribonucleoproteins, and tubulin proteins were up-regulated in the embryonic stage, coincidently with extensive proliferation of neural precursor cells as the major component of the cerebral cortex. Genes related to neurogenesis, including neurite regeneration, neuron development, and synaptic transmission, were more active in adulthood, when the cerebral cortex reached maturity. The many developmentally modulated genes identified by this approach will facilitate further studies of cortical functions.


Subject(s)
Cerebral Cortex/metabolism , DNA, Complementary/biosynthesis , Gene Expression Profiling , Animals , Animals, Newborn , Cell Communication , Cell Differentiation , Cell Proliferation , Cerebral Cortex/embryology , Cerebral Cortex/growth & development , Gene Expression Regulation, Developmental , Heterogeneous-Nuclear Ribonucleoproteins/biosynthesis , Oligonucleotide Array Sequence Analysis , Rats , Rats, Sprague-Dawley , Ribosomal Proteins/biosynthesis , Tubulin/biosynthesis
16.
Mol Ther ; 16(11): 1873-82, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18781144

ABSTRACT

Neural precursor cells (NPCs) are regarded as a promising source of donor cells in transplantation-based therapies for neurodegenerative disorders. However, poor survival and limited neuronal differentiation of the transplanted NPCs remain critical limitations for developing therapeutic strategies. In this study, we investigated the effects of the proneural basic helix-loop-helix (bHLH) transcription factors Mash1 and Neurogenin 2 (Ngn2) in neuronal differentiation and survival of NPCs. Induction of Mash1 or Ngn2 expression strikingly enhanced neuronal differentiation of cultured NPCs in vitro. Ngn2-transduced NPCs underwent a rapid cell cycle arrest, which often accompanies differentiation. In contrast, cells continuously expanded upon Mash1 expression during NPC differentiation. Notably, sonic hedgehog (SHH) was upregulated by Mash1 and mediated the proliferative and survival effects of Mash1 on NPCs. Upon transplantation into adult rat brains, Mash1-expressing NPCs yielded large grafts enriched with neurons compared to control LacZ-transduced NPCs. Interestingly, enhancements in neuronal yield, as well as in donor cell survival, were also achieved by transplanting Ngn2-transduced NPCs. We show that a differentiation stage- and cell density-dependent survival effect of Ngn2 involves neurotrophin3 (NT3)/TrkC-mediated signaling. Together, these findings suggest potential benefits of bHLH gene manipulation to develop successful transplantation strategies for brain disorders.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/genetics , Cell Differentiation/physiology , Cell Survival/physiology , Embryonic Stem Cells/transplantation , Nerve Tissue Proteins/genetics , Neurons/transplantation , Animals , Basic Helix-Loop-Helix Transcription Factors/biosynthesis , Brain/cytology , Cell Proliferation , Cells, Cultured , Embryonic Stem Cells/cytology , Hedgehog Proteins/physiology , In Vitro Techniques , Mice , Nerve Tissue Proteins/biosynthesis , Neurons/cytology , Neurotrophin 3/physiology , Rats , Rats, Sprague-Dawley , Signal Transduction , Transduction, Genetic
17.
J Bioinform Comput Biol ; 5(4): 865-73, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17787060

ABSTRACT

In two-channel microarray experiments, the image analysis extracts red and green fluorescence intensities. The ratio of the two fluorescence intensities represents the relative abundance of the corresponding DNA sequence. The subsequent analysis is performed by taking a log-transformation of this ratio. Therefore, the statistical analyses depend on accuracy of the ratios calculated from the image analysis. However, not many studies have been proposed for developing more reliable ratio statistics. In this paper, we consider a new type of log-transformed ratio statistic. We compare the new ratio statistic with the conventional ratio statistic commonly used in two-channel microarray experiments. First, under the specific log-normal distributional assumption, we compare analytically the new statistics with the conventional ratio statistic. Second, we compare those ratio statistics using a two-channel microarray data obtained by hybridizing a mixture of mouse RNA and yeast in vitro transcript (IVT). Both comparisons show that the proposed ratio statistic performs better than the conventional one.


Subject(s)
Gene Expression Profiling/methods , Models, Statistical , Oligonucleotide Array Sequence Analysis/methods , Pattern Recognition, Automated/methods , Algorithms , Animals , Artifacts , Data Interpretation, Statistical , Genes, Fungal/genetics , Image Interpretation, Computer-Assisted/methods , Mice , RNA/analysis , RNA/genetics , Reproducibility of Results , Sensitivity and Specificity , Software Validation
18.
J Neurochem ; 103(4): 1417-29, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17854346

ABSTRACT

Human embryonic stem (hES) cells can be guided to differentiate into ventral midbrain-type neural precursor (NP) cells that proliferate in vitro by specific mitogens. We investigated the potential of these NP cells derived from hES cells (hES-NP) for the large-scale generation of human dopamine (DA) neurons for functional analyses and therapeutic applications. To address this, hES-NP cells were expanded in vitro for 1.5 months with six passages, and their proliferation and differentiation properties determined over the NP passages. Interestingly, the total hES-NP cell number was increased by > 2 x 10(4)-folds over the in vitro period without alteration of phenotypic gene expression. They also sustained their differentiation capacity toward neuronal cells, exhibiting in vitro pre-synaptic DA neuronal functionality. Furthermore, the hES-NP cells can be cryopreserved without losing their proliferative and developmental potential. Upon transplantation into a Parkinson's disease rat model, the multi-passaged hES-NP cells survived, integrated into the host striatum, and differentiated toward the neuronal cells expressing DA phenotypes. A significant reduction in the amphetamine-induced rotation score of Parkinson's disease rats was observed by the cell transplantation. Taken together, these findings indicate that hES-NP cell expansion is exploitable for a large-scale generation of experimental and transplantable DA neurons of human-origin.


Subject(s)
Cell Differentiation/physiology , Dopamine/metabolism , Embryonic Stem Cells/cytology , Embryonic Stem Cells/metabolism , Neurons/cytology , Neurons/metabolism , Animals , Cell Survival/physiology , Dopamine/physiology , Embryonic Stem Cells/physiology , Female , Humans , Neurons/physiology , Rats , Rats, Sprague-Dawley
19.
Mol Cell Biol ; 27(12): 4293-305, 2007 Jun.
Article in English | MEDLINE | ID: mdl-17438128

ABSTRACT

In the developing mouse brain, the highest Bcl-X(L) expression is seen at the peak of neurogenesis, whereas the peak of Bax expression coincides with the astrogenic period. While such observations suggest an active role of the Bcl-2 family proteins in the generation of neurons and astrocytes, no definitive demonstration has been provided to date. Using combinations of gain- and loss-of-function assays in vivo and in vitro, we provide evidence for instructive roles of these proteins in neuronal and astrocytic fate specification. Specifically, in Bax knockout mice, astrocyte formation was decreased in the developing cortices. Overexpression of Bcl-X(L) and Bax in embryonic cortical precursors induced neural and astrocytic differentiation, respectively, while inhibitory RNAs led to the opposite results. Importantly, inhibition of caspase activity, dimerization, or mitochondrial localization of Bcl-X(L)/Bax proteins indicated that the differentiation effects of Bcl-X(L)/Bax are separable from their roles in cell survival and apoptosis. Lastly, we describe activation of intracellular signaling pathways and expression of basic helix-loop-helix transcriptional factors specific for the Bcl-2 protein-mediated differentiation.


Subject(s)
Cerebral Cortex/cytology , Cerebral Cortex/embryology , Gene Expression Regulation, Developmental , bcl-2-Associated X Protein/metabolism , bcl-X Protein/metabolism , Animals , Astrocytes/cytology , Astrocytes/physiology , Basic Helix-Loop-Helix Transcription Factors/metabolism , Caspase Inhibitors , Cell Differentiation , Cells, Cultured , Coated Materials, Biocompatible/metabolism , Crosses, Genetic , Dimerization , Enzyme Activation , Fibronectins/metabolism , Homozygote , Mice , Mice, Knockout , Mitochondria/metabolism , Mutagenesis, Site-Directed , Neurons/cytology , Neurons/physiology , RNA, Small Interfering/genetics , Retroviridae/genetics , Signal Transduction/physiology , Transduction, Genetic , bcl-2-Associated X Protein/chemistry , bcl-2-Associated X Protein/genetics , bcl-X Protein/chemistry , bcl-X Protein/genetics
20.
Stem Cells ; 25(5): 1252-62, 2007 May.
Article in English | MEDLINE | ID: mdl-17234994

ABSTRACT

Neural precursor (NP) cells from adult mammalian brains can be isolated, expanded in vitro, and potentially used as cell replacement source material for treatment of intractable brain disorders. Reduced ethical concerns, lack of teratoma formation, and possible ex vivo autologous transplantation are critical advantages to using adult NP donor cells over cells from fetal brain tissue or embryonic stem cells. However, the usage of adult NP cells is limited by the ability to induce specific neurochemical phenotypes in these cells. Here, we demonstrate induction of a dopaminergic phenotype in NP cells isolated from the subventricular zone (SVZ) and white matter of rodent adult brains using overexpression of the nuclear receptor Nurr1 in vitro. Forced expression of Nurr1, a transcriptional factor specific to midbrain dopamine (DA) neuron development, caused in the adult cells an acquisition of the DA neurotransmitter phenotype and sufficient differentiation toward morphologically, phenotypically, and ultrastructurally mature DA neurons. Co-expression of neurogenic factor Mash1 and treatment with neurogenic cytokines brain-derived neurotrophic factor and neurotrophin-3 greatly enhanced Nurr1-induced DA neuron yield. The Nurr1-induced DA neurons demonstrated in vitro presynaptic DA neuronal functionality, releasing DA neurotransmitter in response to depolarization stimuli and specific DA reuptake. Furthermore, Nurr1-engineered adult SVZ NP cells survived, integrated, and differentiated into DA neurons in vivo that can reverse the behavioral deficit in the host striatum of parkinsonian rats. These findings open the possibility for the use of precursor cells from adult brains as a cell source for neuronal replacement treatment of Parkinson disease. Disclosure of potential conflicts of interest is found at the end of this article.


Subject(s)
Cerebral Ventricles/cytology , DNA-Binding Proteins/genetics , Dopamine/metabolism , Gene Expression , Neurons/cytology , Stem Cells/cytology , Transcription Factors/genetics , Animals , Cell Differentiation , Cell Separation , Cell Survival , Male , Neurons/transplantation , Neurons/ultrastructure , Nuclear Receptor Subfamily 4, Group A, Member 2 , Phenotype , Rats , Rats, Sprague-Dawley , Stem Cell Transplantation , Synapses/ultrastructure , Transduction, Genetic , Transgenes , Tyrosine 3-Monooxygenase/metabolism
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