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  1. Article ; Online: Investigating microglia-neuron crosstalk by characterizing microglial contamination in human and mouse patch-seq datasets.

    Arbabi, Keon / Jiang, Yiyue / Howard, Derek / Nigam, Anukrati / Inoue, Wataru / Gonzalez-Burgos, Guillermo / Felsky, Daniel / Tripathy, Shreejoy J

    iScience

    2023  Volume 26, Issue 8, Page(s) 107329

    Abstract: Microglia are cells with diverse roles, including the regulation of neuronal excitability. We leveraged Patch-seq to assess the presence and effects of microglia in the local microenvironment of recorded neurons. We first quantified the amounts of ... ...

    Abstract Microglia are cells with diverse roles, including the regulation of neuronal excitability. We leveraged Patch-seq to assess the presence and effects of microglia in the local microenvironment of recorded neurons. We first quantified the amounts of microglial transcripts in three Patch-seq datasets of human and mouse neocortical neurons, observing extensive contamination. Variation in microglial contamination was explained foremost by donor identity, particularly in human samples, and additionally by neuronal cell type identity in mice. Gene set enrichment analysis suggests that microglial contamination is reflective of activated microglia, and that these transcriptional signatures are distinct from those captured via single-nucleus RNA-seq. Finally, neurons with greater microglial contamination differed markedly in their electrophysiological characteristics, including lowered input resistances and more depolarized action potential thresholds. Our results generalize beyond Patch-seq to suggest that activated microglia may be widely present across brain slice preparations and contribute to neuron- and donor-related electrophysiological variability
    Language English
    Publishing date 2023-07-11
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.107329
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Impact of next generation sequencing on our understanding of CAKUT.

    Nigam, Anukrati / Knoers, Nine V A M / Renkema, Kirsten Y

    Seminars in cell & developmental biology

    2018  Volume 91, Page(s) 104–110

    Abstract: Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding ... ...

    Abstract Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.
    MeSH term(s) Animals ; Gene Expression Regulation, Developmental ; Genetic Association Studies/methods ; Genetic Predisposition to Disease/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Kidney/embryology ; Kidney/metabolism ; Kidney/pathology ; Mutation ; Urogenital Abnormalities/diagnosis ; Urogenital Abnormalities/embryology ; Urogenital Abnormalities/genetics ; Vesico-Ureteral Reflux/diagnosis ; Vesico-Ureteral Reflux/embryology ; Vesico-Ureteral Reflux/genetics
    Language English
    Publishing date 2018-09-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2018.08.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2918: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Identification of brain cell types underlying genetic association with word reading and correlated traits.

    Price, Kaitlyn M / Wigg, Karen G / Nigam, Anukrati / Feng, Yu / Blokland, Kirsten / Wilkinson, Margaret / Kerr, Elizabeth N / Guger, Sharon L / Lovett, Maureen W / Strug, Lisa J / Tripathy, Shreejoy J / Barr, Cathy L

    Molecular psychiatry

    2023  Volume 28, Issue 4, Page(s) 1719–1730

    Abstract: Neuroimaging studies implicate multiple cortical regions in reading ability/disability. However, the neural cell types integral to the reading process are unknown. To contribute to this gap in knowledge, we integrated genetic results from genome-wide ... ...

    Abstract Neuroimaging studies implicate multiple cortical regions in reading ability/disability. However, the neural cell types integral to the reading process are unknown. To contribute to this gap in knowledge, we integrated genetic results from genome-wide association studies for word reading (n = 5054) with gene expression datasets from adult/fetal human brain. Linkage disequilibrium score regression (LDSC) suggested that variants associated with word reading were enriched in genes expressed in adult excitatory neurons, specifically layer 5 and 6 FEZF2 expressing neurons and intratelencephalic (IT) neurons, which express the marker genes LINC00507, THEMIS, or RORB. Inhibitory neurons (VIP, SST, and PVALB) were also found. This finding was interesting as neurometabolite studies previously implicated excitatory-inhibitory imbalances in the etiology of reading disabilities (RD). We also tested traits that shared genetic etiology with word reading (previously determined by polygenic risk scores): attention-deficit/hyperactivity disorder (ADHD), educational attainment, and cognitive ability. For ADHD, we identified enrichment in L4 IT adult excitatory neurons. For educational attainment and cognitive ability, we confirmed previous studies identifying multiple subclasses of adult cortical excitatory and inhibitory neurons, as well as astrocytes and oligodendrocytes. For educational attainment and cognitive ability, we also identified enrichment in multiple fetal cortical excitatory and inhibitory neurons, intermediate progenitor cells, and radial glial cells. In summary, this study supports a role of excitatory and inhibitory neurons in reading and excitatory neurons in ADHD and contributes new information on fetal cell types enriched in educational attainment and cognitive ability, thereby improving our understanding of the neurobiological basis of reading/correlated traits.
    MeSH term(s) Adult ; Humans ; Reading ; Genome-Wide Association Study/methods ; Brain ; Dyslexia/genetics ; Cognition ; Attention Deficit Disorder with Hyperactivity/genetics
    Language English
    Publishing date 2023-02-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/s41380-023-01970-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4812: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: An in vitro whole-cell electrophysiology dataset of human cortical neurons.

    Howard, Derek / Chameh, Homeira Moradi / Guet-McCreight, Alexandre / Hsiao, Huan Allen / Vuong, Maggie / Seo, Young Seok / Shah, Prajay / Nigam, Anukrati / Chen, Yuxiao / Davie, Melanie / Hay, Etay / Valiante, Taufik A / Tripathy, Shreejoy J

    GigaScience

    2022  Volume 11

    Abstract: Background: Whole-cell patch-clamp electrophysiology is an essential technique for understanding how single neurons translate their diverse inputs into a functional output. The relative inaccessibility of live human cortical neurons for experimental ... ...

    Abstract Background: Whole-cell patch-clamp electrophysiology is an essential technique for understanding how single neurons translate their diverse inputs into a functional output. The relative inaccessibility of live human cortical neurons for experimental manipulation has made it difficult to determine the unique features of how human cortical neurons differ from their counterparts in other species.
    Findings: We present a curated repository of whole-cell patch-clamp recordings from surgically resected human cortical tissue, encompassing 118 neurons from 35 individuals (age range, 21-59 years; 17 male, 18 female). Recorded human cortical neurons derive from layers 2 and 3 (L2&3), deep layer 3 (L3c), or layer 5 (L5) and are annotated with a rich set of subject and experimental metadata. For comparison, we also provide a limited set of comparable recordings from 21-day-old mice (11 cells from 5 mice). All electrophysiological recordings are provided in the Neurodata Without Borders (NWB) format and are available for further analysis via the Distributed Archives for Neurophysiology Data Integration online repository. The associated data conversion code is made publicly available and can help others in converting electrophysiology datasets to the open NWB standard for general reuse.
    Conclusion: These data can be used for novel analyses of biophysical characteristics of human cortical neurons, including in cross-species or cross-lab comparisons or in building computational models of individual human neurons.
    MeSH term(s) Humans ; Male ; Female ; Mice ; Animals ; Young Adult ; Adult ; Middle Aged ; Patch-Clamp Techniques ; Neurons/physiology ; Electrophysiology
    Language English
    Publishing date 2022-12-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giac108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: mTOR-Activating Mutations in

    Schlingmann, Karl P / Jouret, François / Shen, Kuang / Nigam, Anukrati / Arjona, Francisco J / Dafinger, Claudia / Houillier, Pascal / Jones, Deborah P / Kleinerüschkamp, Felix / Oh, Jun / Godefroid, Nathalie / Eltan, Mehmet / Güran, Tülay / Burtey, Stéphane / Parotte, Marie-Christine / König, Jens / Braun, Alina / Bos, Caro / Ibars Serra, Maria /
    Rehmann, Holger / Zwartkruis, Fried J T / Renkema, Kirsten Y / Klingel, Karin / Schulze-Bahr, Eric / Schermer, Bernhard / Bergmann, Carsten / Altmüller, Janine / Thiele, Holger / Beck, Bodo B / Dahan, Karin / Sabatini, David / Liebau, Max C / Vargas-Poussou, Rosa / Knoers, Nine V A M / Konrad, Martin / de Baaij, Jeroen H F

    Journal of the American Society of Nephrology : JASN

    2021  Volume 32, Issue 11, Page(s) 2885–2899

    Abstract: Background: Over the last decade, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, approximately 20% of all patients with tubulopathy lack a genetic ... ...

    Abstract Background: Over the last decade, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, approximately 20% of all patients with tubulopathy lack a genetic diagnosis.
    Methods: We performed whole-exome and -genome sequencing of a patient cohort with a novel, inherited, salt-losing tubulopathy; hypomagnesemia; and dilated cardiomyopathy. We also conducted subsequent
    Results: In eight children from unrelated families with a tubulopathy characterized by hypomagnesemia, hypokalemia, salt wasting, and nephrocalcinosis, we identified heterozygous missense variants in
    Conclusions: Our findings establish a novel disease, which we call autosomal dominant kidney hypomagnesemia (ADKH-RRAGD), that combines an electrolyte-losing tubulopathy and dilated cardiomyopathy. The condition is caused by variants in the
    MeSH term(s) Cardiomyopathy, Dilated/genetics ; Cardiomyopathy, Dilated/metabolism ; Female ; HEK293 Cells ; Humans ; Hypercalciuria/genetics ; Hypercalciuria/metabolism ; Kidney Diseases/genetics ; Kidney Diseases/metabolism ; Kidney Tubules, Distal/metabolism ; Male ; Models, Molecular ; Monomeric GTP-Binding Proteins/genetics ; Mutation, Missense ; Natriuresis/genetics ; Nephrocalcinosis/genetics ; Nephrocalcinosis/metabolism ; Pedigree ; Protein Conformation ; Renal Tubular Transport, Inborn Errors/genetics ; Renal Tubular Transport, Inborn Errors/metabolism ; Seizures/genetics ; Seizures/metabolism ; Signal Transduction ; TOR Serine-Threonine Kinases/metabolism ; Exome Sequencing ; Whole Genome Sequencing
    Chemical Substances RRAGD protein, human ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.11.1) ; Monomeric GTP-Binding Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2021-10-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1085942-1
    ISSN 1533-3450 ; 1046-6673
    ISSN (online) 1533-3450
    ISSN 1046-6673
    DOI 10.1681/ASN.2021030333
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3344: Show issues Location:
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