LIVIVO - Search results -

Search results

Result 1 - 10 of total 261

Search options

Article: Cell type-specific enrichment of somatic aneuploidy in the mammalian brain.

Mukamel, Eran A / Liu, Hanqing / Behrens, M Margarita / Ecker, Joseph R

bioRxiv : the preprint server for biology

2023

Abstract: Somatic mutations alter the genomes of a subset of an individual's brain ... ...

Abstract	Somatic mutations alter the genomes of a subset of an individual's brain cells
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.18.572285
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Joint profiling of histone modifications and transcriptome in single cells from mouse brain.

Zhu, Chenxu / Zhang, Yanxiao / Li, Yang Eric / Lucero, Jacinta / Behrens, M Margarita / Ren, Bing

Nature methods

2021 Volume 18, Issue 3, Page(s) 283–292

Abstract: Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. ... ...

Abstract	Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissues lack single-cell resolution. Here we describe an ultra-high-throughput method, Paired-Tag, for joint profiling of histone modifications and transcriptome in single cells to produce cell-type-resolved maps of chromatin state and transcriptome in complex tissues. We used this method to profile five histone modifications jointly with transcriptome in the adult mouse frontal cortex and hippocampus. Integrative analysis of the resulting maps identified distinct groups of genes subject to divergent epigenetic regulatory mechanisms. Our single-cell multiomics approach enables comprehensive analysis of chromatin state and gene regulation in complex tissues and characterization of gene regulatory programs in the constituent cell types.
MeSH term(s)	Animals ; Cell Line, Tumor ; Chromatin/metabolism ; Epigenesis, Genetic/genetics ; Frontal Lobe/cytology ; Frontal Lobe/metabolism ; Gene Expression Profiling ; Gene Expression Regulation/genetics ; HeLa Cells ; Hippocampus/cytology ; Hippocampus/metabolism ; Histone Code/genetics ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Protein Processing, Post-Translational ; Regulatory Sequences, Nucleic Acid/genetics ; Single-Cell Analysis ; Transcriptome/genetics
Chemical Substances	Chromatin
Language	English
Publishing date	2021-02-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-021-01060-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6022: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex.

Zemke, Nathan R / Armand, Ethan J / Wang, Wenliang / Lee, Seoyeon / Zhou, Jingtian / Li, Yang Eric / Liu, Hanqing / Tian, Wei / Nery, Joseph R / Castanon, Rosa G / Bartlett, Anna / Osteen, Julia K / Li, Daofeng / Zhuo, Xiaoyu / Xu, Vincent / Chang, Lei / Dong, Keyi / Indralingam, Hannah S / Rink, Jonathan A /

Xie, Yang / Miller, Michael / Krienen, Fenna M / Zhang, Qiangge / Taskin, Naz / Ting, Jonathan / Feng, Guoping / McCarroll, Steven A / Callaway, Edward M / Wang, Ting / Lein, Ed S / Behrens, M Margarita / Ecker, Joseph R / Ren, Bing

Nature

2024 Volume 625, Issue 7996, Page(s) E26

Language	English
Publishing date	2024-01-09
Publishing country	England
Document type	Published Erratum
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-07013-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 9: Show issues
Zs.MO 244: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Abnormal Gamma Oscillations in N-Methyl-D-Aspartate Receptor Hypofunction Models of Schizophrenia.

Jadi, Monika P / Behrens, M Margarita / Sejnowski, Terrence J

Biological psychiatry

2015 Volume 79, Issue 9, Page(s) 716–726

Abstract: N-methyl-D-aspartate receptor (NMDAR) hypofunction in parvalbumin-expressing (PV+) inhibitory neurons (INs) may contribute to symptoms in patients with schizophrenia (SZ). This hypothesis was inspired by studies in humans involving NMDAR antagonists that ...

Abstract	N-methyl-D-aspartate receptor (NMDAR) hypofunction in parvalbumin-expressing (PV+) inhibitory neurons (INs) may contribute to symptoms in patients with schizophrenia (SZ). This hypothesis was inspired by studies in humans involving NMDAR antagonists that trigger SZ symptoms. Animal models of SZ using neuropharmacology and genetic knockouts have successfully replicated some of the key observations in human subjects involving alteration of gamma band oscillations (GBO) observed in electroencephalography and magnetoencephalography signals. However, it remains to be seen if NMDAR hypofunction in PV+ neurons is fundamental to the phenotype observed in these models. In this review, we discuss some of the key computational models of GBO and their predictions in the context of NMDAR hypofunction in INs. While PV+ INs have been the main focus of SZ studies in animal models, we also discuss the implications of NMDAR hypofunction in other types of INs using computational models for GBO modulation in the visual cortex.
MeSH term(s)	Action Potentials ; Animals ; Cerebral Cortex/physiopathology ; Electroencephalography ; GABAergic Neurons/metabolism ; GABAergic Neurons/physiology ; Gamma Rhythm ; Humans ; Interneurons/metabolism ; Interneurons/physiology ; Models, Neurological ; Parvalbumins/metabolism ; Receptors, N-Methyl-D-Aspartate/genetics ; Receptors, N-Methyl-D-Aspartate/physiology ; Schizophrenia/physiopathology ; gamma-Aminobutyric Acid/physiology
Chemical Substances	Parvalbumins ; Receptors, N-Methyl-D-Aspartate ; gamma-Aminobutyric Acid (56-12-2)
Language	English
Publishing date	2015-07-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	209434-4
ISSN	1873-2402 ; 0006-3223
ISSN (online)	1873-2402
ISSN	0006-3223
DOI	10.1016/j.biopsych.2015.07.005
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 720: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Ketamine independently modulated power and phase-coupling of theta oscillations in Sp4 hypomorphic mice.

Wang, Xin / Pinto-Duarte, António / Behrens, M Margarita / Zhou, Xianjin / Sejnowski, Terrence J

PloS one

2018 Volume 13, Issue 3, Page(s) e0193446

Abstract: Reduced expression of Sp4, the murine homolog of human SP4, a risk gene of multiple psychiatric disorders, led to N-methyl-D-aspartate (NMDA) hypofunction in mice, producing behavioral phenotypes reminiscent of schizophrenia, including hypersensitivity ... ...

Abstract	Reduced expression of Sp4, the murine homolog of human SP4, a risk gene of multiple psychiatric disorders, led to N-methyl-D-aspartate (NMDA) hypofunction in mice, producing behavioral phenotypes reminiscent of schizophrenia, including hypersensitivity to ketamine. As accumulating evidence on molecular mechanisms and behavioral phenotypes established Sp4 hypomorphism as a promising animal model, systems-level neural circuit mechanisms of Sp4 hypomorphism, especially network dynamics underlying cognitive functions, remain poorly understood. We attempted to close this gap in knowledge in the present study by recording multi-channel epidural electroencephalogram (EEG) from awake behaving wildtype and Sp4 hypomorphic mice. We characterized cortical theta-band power and phase-coupling phenotypes, a known neural circuit substrate underlying cognitive functions, and further studied the effects of a subanesthetic dosage of ketamine on theta abnormalities unique to Sp4 hypomorphism. Sp4 hypomorphic mice had markedly elevated theta power localized frontally and parietally, a more pronounced theta phase progression along the neuraxis, and a stronger frontal-parietal theta coupling. Acute subanesthetic ketamine did not affect theta power in wildtype animals but significantly reduced it in Sp4 hypomorphic mice, nearly completely neutralizing their excessive frontal/parietal theta power. Ketamine did not significantly alter cortical theta phase progression in either wildtype or Sp4 hypomorphic animals, but significantly strengthened cortical theta phase-coupling in wildtype, but not in Sp4 hypomorphic animals. Our results suggested that the resting-state phenotypes of cortical theta oscillations unique to Sp4 hypomorphic mice closely mimicked a schizophrenic endophenotype. Further, ketamine independently modulated Sp4 hypomorphic anomalies in theta power and phase-coupling, suggesting separate underlying neural circuit mechanisms.
MeSH term(s)	Animals ; Brain/drug effects ; Brain/physiology ; Electroencephalography/methods ; Excitatory Amino Acid Antagonists/pharmacology ; Female ; Ketamine/pharmacology ; Male ; Mice, Inbred C57BL ; Mice, Transgenic ; Phenotype ; Sp4 Transcription Factor/deficiency ; Sp4 Transcription Factor/genetics ; Theta Rhythm/drug effects ; Theta Rhythm/physiology
Chemical Substances	Excitatory Amino Acid Antagonists ; Sp4 Transcription Factor ; Sp4 protein, mouse ; Ketamine (690G0D6V8H)
Language	English
Publishing date	2018-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0193446
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.

Xie, Fangming / Armand, Ethan J / Yao, Zizhen / Liu, Hanqing / Bartlett, Anna / Behrens, M Margarita / Li, Yang Eric / Lucero, Jacinta D / Luo, Chongyuan / Nery, Joseph R / Pinto-Duarte, Antonio / Poirion, Olivier B / Preissl, Sebastian / Rivkin, Angeline C / Tasic, Bosiljka / Zeng, Hongkui / Ren, Bing / Ecker, Joseph R / Mukamel, Eran A

Cell genomics

2023 Volume 3, Issue 7, Page(s) 100342

Abstract: Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic ... ...

Abstract	Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our predictions by comparing them with chromatin conformation data and causal enhancer perturbation experiments. Our study shows how controlling for gene co-expression enables robust enhancer-gene linkage using single-cell sequencing data.
Language	English
Publishing date	2023-06-19
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2023.100342
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Ketamine independently modulated power and phase-coupling of theta oscillations in Sp4 hypomorphic mice.

Xin Wang / António Pinto-Duarte / M Margarita Behrens / Xianjin Zhou / Terrence J Sejnowski

PLoS ONE, Vol 13, Iss 3, p e

2018 Volume 0193446

Abstract	Reduced expression of Sp4, the murine homolog of human SP4, a risk gene of multiple psychiatric disorders, led to N-methyl-D-aspartate (NMDA) hypofunction in mice, producing behavioral phenotypes reminiscent of schizophrenia, including hypersensitivity to ketamine. As accumulating evidence on molecular mechanisms and behavioral phenotypes established Sp4 hypomorphism as a promising animal model, systems-level neural circuit mechanisms of Sp4 hypomorphism, especially network dynamics underlying cognitive functions, remain poorly understood. We attempted to close this gap in knowledge in the present study by recording multi-channel epidural electroencephalogram (EEG) from awake behaving wildtype and Sp4 hypomorphic mice. We characterized cortical theta-band power and phase-coupling phenotypes, a known neural circuit substrate underlying cognitive functions, and further studied the effects of a subanesthetic dosage of ketamine on theta abnormalities unique to Sp4 hypomorphism. Sp4 hypomorphic mice had markedly elevated theta power localized frontally and parietally, a more pronounced theta phase progression along the neuraxis, and a stronger frontal-parietal theta coupling. Acute subanesthetic ketamine did not affect theta power in wildtype animals but significantly reduced it in Sp4 hypomorphic mice, nearly completely neutralizing their excessive frontal/parietal theta power. Ketamine did not significantly alter cortical theta phase progression in either wildtype or Sp4 hypomorphic animals, but significantly strengthened cortical theta phase-coupling in wildtype, but not in Sp4 hypomorphic animals. Our results suggested that the resting-state phenotypes of cortical theta oscillations unique to Sp4 hypomorphic mice closely mimicked a schizophrenic endophenotype. Further, ketamine independently modulated Sp4 hypomorphic anomalies in theta power and phase-coupling, suggesting separate underlying neural circuit mechanisms.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex.

Zemke, Nathan R / Armand, Ethan J / Wang, Wenliang / Lee, Seoyeon / Zhou, Jingtian / Li, Yang Eric / Liu, Hanqing / Tian, Wei / Nery, Joseph R / Castanon, Rosa G / Bartlett, Anna / Osteen, Julia K / Li, Daofeng / Zhuo, Xiaoyu / Xu, Vincent / Miller, Michael / Krienen, Fenna M / Zhang, Qiangge / Taskin, Naz /

Ting, Jonathan / Feng, Guoping / McCarroll, Steven A / Callaway, Edward M / Wang, Ting / Behrens, M Margarita / Lein, Ed S / Ecker, Joseph R / Ren, Bing

bioRxiv : the preprint server for biology

2023

Abstract: Sequence divergence ... ...

Abstract	Sequence divergence of
Language	English
Publishing date	2023-04-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.08.536119
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Iterative single-cell multi-omic integration using online learning.

Gao, Chao / Liu, Jialin / Kriebel, April R / Preissl, Sebastian / Luo, Chongyuan / Castanon, Rosa / Sandoval, Justin / Rivkin, Angeline / Nery, Joseph R / Behrens, Margarita M / Ecker, Joseph R / Ren, Bing / Welch, Joshua D

Nature biotechnology

2021 Volume 39, Issue 8, Page(s) 1000–1007

Abstract: Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for ... ...

Abstract	Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for integrating large, diverse and continually arriving single-cell datasets. Our approach scales to arbitrarily large numbers of cells using fixed memory, iteratively incorporates new datasets as they are generated and allows many users to simultaneously analyze a single copy of a large dataset by streaming it over the internet. Iterative data addition can also be used to map new data to a reference dataset. Comparisons with previous methods indicate that the improvements in efficiency do not sacrifice dataset alignment and cluster preservation performance. We demonstrate the effectiveness of online iNMF by integrating more than 1 million cells on a standard laptop, integrating large single-cell RNA sequencing and spatial transcriptomic datasets, and iteratively constructing a single-cell multi-omic atlas of the mouse motor cortex.
MeSH term(s)	Algorithms ; Animals ; Computational Biology/methods ; Machine Learning ; Mice ; Multivariate Analysis ; Single-Cell Analysis/methods ; Transcriptome/genetics
Language	English
Publishing date	2021-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-021-00867-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 137: Show issues
Zs.MG 43: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Conserved and divergent gene regulatory programs of the mammalian neocortex.

Nature

2023 Volume 624, Issue 7991, Page(s) 390–402

Abstract: Divergence of cis-regulatory elements drives species-specific ... ...

Abstract	Divergence of cis-regulatory elements drives species-specific traits
MeSH term(s)	Animals ; Humans ; Mice ; Callithrix/genetics ; Chromatin/genetics ; Chromatin/metabolism ; Conserved Sequence/genetics ; DNA Methylation ; DNA Transposable Elements/genetics ; Epigenome ; Evolution, Molecular ; Gene Expression Regulation/genetics ; Gene Regulatory Networks ; Macaca/genetics ; Mammals/genetics ; Motor Cortex/cytology ; Motor Cortex/metabolism ; Multiomics ; Neocortex/cytology ; Neocortex/metabolism ; Regulatory Sequences, Nucleic Acid/genetics ; Single-Cell Analysis ; Transcription Factors/metabolism ; Genetic Variation/genetics
Chemical Substances	Chromatin ; DNA Transposable Elements ; Transcription Factors
Language	English
Publishing date	2023-12-13
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06819-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 9: Show issues
Zs.MO 244: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito