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  1. Article ; Online: Pre-existing antibody allows for maturation of new B cells in 'recall' germinal centres.

    Herb, Jake / Curotto de Lafaille, Maria

    Nature reviews. Immunology

    2024  Volume 24, Issue 4, Page(s) 234

    MeSH term(s) Humans ; B-Lymphocytes ; Germinal Center ; Antibodies
    Chemical Substances Antibodies
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2062776-2
    ISSN 1474-1741 ; 1474-1733
    ISSN (online) 1474-1741
    ISSN 1474-1733
    DOI 10.1038/s41577-024-01012-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5565: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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    Zs.MG 34: Show issues

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  2. Article: Genetic and bioinformatic analyses reveal transcriptional networks underlying dual genomic coordination of mitochondrial biogenesis.

    Zhang, Fan / Lee, Annie / Freitas, Anna / Herb, Jake / Wang, Zongheng / Gupta, Snigdha / Chen, Zhe / Xu, Hong

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Mitochondrial genome encodes handful genes of respiratory chain complexes, whereas all the remaining mitochondrial proteins are encoded on the nuclear genome. However, the mechanisms coordinating these two genomes to control mitochondrial biogenesis ... ...

    Abstract Mitochondrial genome encodes handful genes of respiratory chain complexes, whereas all the remaining mitochondrial proteins are encoded on the nuclear genome. However, the mechanisms coordinating these two genomes to control mitochondrial biogenesis remain largely unknown. To identify transcription circuits involved in these processes, we performed a candidate RNAi screen in developing eyes that had reduced mitochondrial DNA contents. We reasoned that impaired mitochondrial biogenesis would synergistically interact with mtDNA deficiency in disrupting tissue development. Over 638 transcription factors annotated in the fly genome, we identified 77 transcription factors that may be involved in mitochondrial genome maintenance and gene expression. Additional genetic and genomic analyses revealed that a novel transcription factor, CG1603, and its upstream factor YL-1 are essential for mitochondrial biogenesis. We constructed a regulator network among positive hits using the published CHIP-seq data. The network analysis revealed extensive connections, and complex hierarchical organization underlying the transcription regulation of mitochondrial biogenesis.
    Language English
    Publishing date 2024-01-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.25.577217
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii.

    Hackley, Rylee K / Hwang, Sungmin / Herb, Jake T / Bhanap, Preeti / Lam, Katie / Vreugdenhil, Angie / Darnell, Cynthia L / Pastor, Mar Martinez / Martin, Johnathan H / Maupin-Furlow, Julie A / Schmid, Amy K

    Molecular microbiology

    2024  Volume 121, Issue 4, Page(s) 742–766

    Abstract: Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism ... ...

    Abstract Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.
    MeSH term(s) Haloferax volcanii/genetics ; Glucose/metabolism ; Metabolic Networks and Pathways ; Membrane Glycoproteins/metabolism ; Phenotype ; Archaeal Proteins/metabolism
    Chemical Substances Glucose (IY9XDZ35W2) ; Membrane Glycoproteins ; Archaeal Proteins
    Language English
    Publishing date 2024-01-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/mmi.15225
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2502: Show issues Location:
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  4. Article ; Online: Generation of a mitochondrial protein compendium in

    Freitas, Anna V / Herb, Jake T / Pan, Miao / Chen, Yong / Gucek, Marjan / Jin, Tian / Xu, Hong

    iScience

    2022  Volume 25, Issue 5, Page(s) 104332

    Abstract: The social ... ...

    Abstract The social ameba
    Language English
    Publishing date 2022-04-29
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.104332
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  5. Article ; Online: Investigating the binding of acridine, acridine orange, and acridine yellow G to humic acid through fluorescence quenching.

    Herb, Jake T / Anderson, Bruce D

    Applied spectroscopy

    2013  Volume 67, Issue 7, Page(s) 752–756

    Abstract: A fluorescence quenching method was used to determine the equilibrium binding constants for the association of acridine, acridine orange, and acridine yellow G to humic acid. The fluorescence of each polycyclic aromatic nitrogen heterocycle (PANH) was ... ...

    Abstract A fluorescence quenching method was used to determine the equilibrium binding constants for the association of acridine, acridine orange, and acridine yellow G to humic acid. The fluorescence of each polycyclic aromatic nitrogen heterocycle (PANH) was monitored as aliquots of humic acid were added, and a Stern-Volmer plot was produced in which the slope is the equilibrium constant of the binding reaction. The quenching experiments were performed at temperatures of 30, 35, 40, and 45 °C. A van't Hoff plot generated from the equilibrium binding constants as a function of temperature for a given PANH resulted in a linear plot. Calculation of the ΔHbinding, ΔGbinding, and ΔSbinding for each PANH leads to the conclusion that the equilibrium binding constant, and ΔGbinding, may be predictors of bioavailability. The other thermodynamic quantities, ΔHbinding and ΔSbinding, are helpful in understanding the relative binding of the compounds. For example, acridine yellow G appears to be the least bioavailable of the three PANHs studied because of its strong ΔHbinding = -29.8 kJ/mol, which leads to ΔGbinding = -0.71 kJ/mol. While acridine orange and acridine have similar ΔHbinding values, acridine orange is more likely to bind to humic acid because the ΔSbinding for the process is less negative. Thermodynamic values and equilibrium binding constants for all three compounds are reported.
    MeSH term(s) Acridines/analysis ; Acridines/chemistry ; Algorithms ; Binding Sites ; Humic Substances/analysis ; Spectrometry, Fluorescence/methods
    Chemical Substances Acridines ; Humic Substances
    Language English
    Publishing date 2013-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1943-3530
    ISSN (online) 1943-3530
    DOI 10.1366/12-06795
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: A fluorinated dialkoxide-based magnesium-ion electrolyte

    Herb, Jake T / Nist-Lund, Carl A / Arnold, Craig B

    Journal of materials chemistry A. 2017 May 3, v. 5, no. 17

    2017  

    Abstract: Efficient large scale electrochemical energy storage systems, such as those based on multivalent ions, are a prerequisite for the realization of intermittent renewable energy sources. From the perspectives of both cost and environmental concerns, it is ... ...

    Abstract Efficient large scale electrochemical energy storage systems, such as those based on multivalent ions, are a prerequisite for the realization of intermittent renewable energy sources. From the perspectives of both cost and environmental concerns, it is of critical importance that components of these systems are synthesized using sustainable chemical processes starting from their initial conception. Herein, we report on a fluorinated dialkoxide-based magnesium-ion electrolyte that is synthesized through an atom-efficient and scalable process without the use of any metal alkyls. The electrolyte composition results in high solution conductivity (4.77 mS cm−1 at 26.3 °C), low overpotentials, ca. 100% coulombic efficiency for electrodeposition/dissolution, and good performance in full battery cells using Chevrel phase Mo6S8.
    Keywords batteries ; electrochemistry ; energy ; green chemistry ; ions ; renewable energy sources ; sulfides
    Language English
    Dates of publication 2017-0503
    Size p. 7801-7805.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 2702232-8
    ISSN 2050-7496 ; 2050-7488
    ISSN (online) 2050-7496
    ISSN 2050-7488
    DOI 10.1039/c7ta01578j
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes.

    Humphrey, Jack / Venkatesh, Sanan / Hasan, Rahat / Herb, Jake T / de Paiva Lopes, Katia / Küçükali, Fahri / Byrska-Bishop, Marta / Evani, Uday S / Narzisi, Giuseppe / Fagegaltier, Delphine / Sleegers, Kristel / Phatnani, Hemali / Knowles, David A / Fratta, Pietro / Raj, Towfique

    Nature neuroscience

    2022  Volume 26, Issue 1, Page(s) 150–162

    Abstract: Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease affecting motor neurons in the brain and spinal cord. In this study, we investigated gene expression changes in ALS via RNA sequencing in 380 postmortem samples from ... ...

    Abstract Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease affecting motor neurons in the brain and spinal cord. In this study, we investigated gene expression changes in ALS via RNA sequencing in 380 postmortem samples from cervical, thoracic and lumbar spinal cord segments from 154 individuals with ALS and 49 control individuals. We observed an increase in microglia and astrocyte gene expression, accompanied by a decrease in oligodendrocyte gene expression. By creating a gene co-expression network in the ALS samples, we identified several activated microglia modules that negatively correlate with retrospective disease duration. We mapped molecular quantitative trait loci and found several potential ALS risk loci that may act through gene expression or splicing in the spinal cord and assign putative cell types for FNBP1, ACSL5, SH3RF1 and NFASC. Finally, we outline how common genetic variants associated with splicing of C9orf72 act as proxies for the well-known repeat expansion, and we use the same mechanism to suggest ATXN3 as a putative risk gene.
    MeSH term(s) Humans ; Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/metabolism ; Neurodegenerative Diseases/metabolism ; Retrospective Studies ; Transcriptome ; Spinal Cord/metabolism
    Language English
    Publishing date 2022-12-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1420596-8
    ISSN 1546-1726 ; 1097-6256
    ISSN (online) 1546-1726
    ISSN 1097-6256
    DOI 10.1038/s41593-022-01205-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4891: Show issues Location:
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    Zs.MG 67: Show issues

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  8. Article ; Online: Tuning Sodium Ion Conductivity in the Layered Honeycomb Oxide Na(3-x)Sn(2-x)Sb(x)NaO6.

    Smaha, Rebecca W / Roudebush, John H / Herb, Jake T / Seibel, Elizabeth M / Krizan, Jason W / Fox, Gary M / Huang, Qingzhen / Arnold, Craig B / Cava, Robert J

    Inorganic chemistry

    2015  Volume 54, Issue 16, Page(s) 7985–7991

    Abstract: A series of compounds with the composition Na(3-x)Sn(2-x)Sb(x)NaO6 (x = 0.0, 0.2, 0.4, 0.6, 0.7, 0.8, 0.9, and 1.0) has been prepared by solid-state reaction and characterized by powder X-ray diffraction, neutron diffraction (for x = 0.0), and impedance ... ...

    Abstract A series of compounds with the composition Na(3-x)Sn(2-x)Sb(x)NaO6 (x = 0.0, 0.2, 0.4, 0.6, 0.7, 0.8, 0.9, and 1.0) has been prepared by solid-state reaction and characterized by powder X-ray diffraction, neutron diffraction (for x = 0.0), and impedance spectroscopy. The compounds have a layered structure derived from that of α-NaFeO2, with alternating Na3 planes and NaSn2O6 slabs with honeycomb in-plane ordering. The structure of the parent compound, Na2SnO3, has been determined as a two-layer honeycomb in monoclinic space group C2/c. Due to charge neutrality requirements, the substitution of Sb(5+) for Sn(4+) creates sodium site vacancies that facilitate high sodium ion mobility. A decrease in layer stacking disorder is also observed. The conductivity increases linearly with x and has a maximum at x = 0.8 (1.43 × 10(-3) S/cm at 500 °C with suboptimal sample densities). This material may be of interest as a solid Na ion electrolyte.
    Language English
    Publishing date 2015-08-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1484438-2
    ISSN 1520-510X ; 0020-1669
    ISSN (online) 1520-510X
    ISSN 0020-1669
    DOI 10.1021/acs.inorgchem.5b01186
    Database MEDical Literature Analysis and Retrieval System OnLINE

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