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  1. Article ; Online: Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.

    Ferreira, Renata C / Rodrigues, Camila R / Broach, James R / Briones, Marcelo R S

    International journal of molecular sciences

    2024  Volume 25, Issue 7

    Abstract: The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals ... ...

    Abstract The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
    MeSH term(s) Humans ; Animals ; Neanderthals/genetics ; Genome, Mitochondrial ; Mutation ; Alzheimer Disease ; Nucleotides
    Chemical Substances Nucleotides
    Language English
    Publishing date 2024-03-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25073785
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  2. Article ; Online: Microbial adaptive evolution.

    Shi, Aiqin / Fan, Feiyu / Broach, James R

    Journal of industrial microbiology & biotechnology

    2021  Volume 49, Issue 2

    Abstract: Bacterial species can adapt to significant changes in their environment by mutation followed by selection, a phenomenon known as "adaptive evolution." With the development of bioinformatics and genetic engineering, research on adaptive evolution has ... ...

    Abstract Bacterial species can adapt to significant changes in their environment by mutation followed by selection, a phenomenon known as "adaptive evolution." With the development of bioinformatics and genetic engineering, research on adaptive evolution has progressed rapidly, as have applications of the process. In this review, we summarize various mechanisms of bacterial adaptive evolution, the technologies used for studying it, and successful applications of the method in research and industry. We particularly highlight the contributions of Dr. L. O. Ingram. Microbial adaptive evolution has significant impact on our society not only from its industrial applications, but also in the evolution, emergence, and control of various pathogens.
    MeSH term(s) Adaptation, Physiological/genetics ; Bacteria/genetics ; Evolution, Molecular
    Language English
    Publishing date 2021-10-21
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 1482484-X
    ISSN 1476-5535 ; 1367-5435
    ISSN (online) 1476-5535
    ISSN 1367-5435
    DOI 10.1093/jimb/kuab076
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  3. Article: Human

    Smith, Danielle / Bastug, Kristen / Burgoine, Kathy / Broach, James R / Hehnly, Christine / Morton, Sarah U / Osman, Marwan / Schiff, Steven J / Ericson, Jessica E

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Neonatal infections due ... ...

    Abstract Neonatal infections due to
    Language English
    Publishing date 2023-09-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.19.23295794
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Gut microbiome dynamics and associations with mortality in critically ill patients.

    Salameh, Tarik J / Roth, Katharine / Schultz, Lisa / Ma, Zhexi / Bonavia, Anthony S / Broach, James R / Hu, Bin / Howrylak, Judie A

    Gut pathogens

    2023  Volume 15, Issue 1, Page(s) 66

    Abstract: Background: Critical illness and care within the intensive care unit (ICU) leads to profound changes in the composition of the gut microbiome. The impact of such changes on the patients and their subsequent disease course remains uncertain. We ... ...

    Abstract Background: Critical illness and care within the intensive care unit (ICU) leads to profound changes in the composition of the gut microbiome. The impact of such changes on the patients and their subsequent disease course remains uncertain. We hypothesized that specific changes in the gut microbiome would be more harmful than others, leading to increased mortality in critically ill patients.
    Methods: This was a prospective cohort study of critically ill adults in the ICU. We obtained rectal swabs from 52 patients and assessed the composition the gut microbiome using 16 S rRNA gene sequencing. We followed patients throughout their ICU course and evaluated their mortality rate at 28 days following admission to the ICU. We used selbal, a machine learning method, to identify the balance of microbial taxa most closely associated with 28-day mortality.
    Results: We found that a proportional ratio of four taxa could be used to distinguish patients with a higher risk of mortality from patients with a lower risk of mortality (p = .02). We named this binarized ratio our microbiome mortality index (MMI). Patients with a high MMI had a higher 28-day mortality compared to those with a low MMI (hazard ratio, 2.2, 95% confidence interval 1.1-4.3), and remained significant after adjustment for other ICU mortality predictors, including the presence of the acute respiratory distress syndrome (ARDS) and the Acute Physiology and Chronic Health Evaluation (APACHE II) score (hazard ratio, 2.5, 95% confidence interval 1.4-4.7). High mortality was driven by taxa from the Anaerococcus (genus) and Enterobacteriaceae (family), while lower mortality was driven by Parasutterella and Campylobacter (genera).
    Conclusions: Dysbiosis in the gut of critically ill patients is an independent risk factor for increased mortality at 28 days after adjustment for clinically significant confounders. Gut dysbiosis may represent a potential therapeutic target for future ICU interventions.
    Language English
    Publishing date 2023-12-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2478277-4
    ISSN 1757-4749
    ISSN 1757-4749
    DOI 10.1186/s13099-023-00567-8
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  5. Article ; Online: Phosphorylation and nuclear transit modulate the balance between normal function and terminal aggregation of the yeast RNA-binding protein Ssd1.

    Kurischko, Cornelia / Broach, James R

    Molecular biology of the cell

    2017  Volume 28, Issue 22, Page(s) 3057–3069

    Abstract: Yeast Ssd1 is an RNA-binding protein that shuttles between the nucleus and cytoplasm. Ssd1 interacts with its target mRNAs initially during transcription by binding through ... ...

    Abstract Yeast Ssd1 is an RNA-binding protein that shuttles between the nucleus and cytoplasm. Ssd1 interacts with its target mRNAs initially during transcription by binding through its
    Language English
    Publishing date 2017-11-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1098979-1
    ISSN 1939-4586 ; 1059-1524
    ISSN (online) 1939-4586
    ISSN 1059-1524
    DOI 10.1091/mbc.E17-02-0100
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2853: Show issues Location:
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  6. Book ; Collection: The molecular and cellular biology of the yeast Saccharomyces

    Broach, James R.

    (Cold Spring Harbor monograph series ; 21)

    1991  

    Author's details ed. by James R. Broach
    Series title Cold Spring Harbor monograph series ; 21
    Collection
    Language English
    Dates of publication 1991-9999
    Publisher Cold Spring Harbor Laboratory Press
    Publishing place New York
    Publishing country Great Britain
    Document type Book ; Collection (display volumes)
    HBZ-ID HT006246588
    Database Catalogue ZB MED Nutrition, Environment, Agriculture

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  7. Book: The molecular and cellular biology of the yeast Saccharomyces / 1

    Broach, James R.

    1991  

    Author's details ed. by James R. Broach
    Collection The molecular and cellular biology of the yeast Saccharomyces
    Keywords Saccharomyces ; Cytologie
    Subject Zellbiologie ; Zellenlehre ; Zellforschung ; Zellkunde ; Zelluologie ; Zytologie ; Zelle
    Language English
    Size IX, 826 S. : Ill., graph. Darst.
    Publisher Cold Spring Harbor Laboratory Press
    Publishing place New York
    Publishing country Great Britain
    Document type Book
    HBZ-ID HT006263716
    ISBN 0-87969-355-X ; 0879693060 ; 978-0-87969-355-8 ; 9780879693060
    Database Catalogue ZB MED Nutrition, Environment, Agriculture

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    In stock of ZB MED Bonn / Germany

    Shelf markLoan statusLocation
    948/2088 available for loan (reading room) Freihandmagazin (U1)

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  8. Article ; Online: Nutritional control of growth and development in yeast.

    Broach, James R

    Genetics

    2012  Volume 192, Issue 1, Page(s) 73–105

    Abstract: Availability of key nutrients, such as sugars, amino acids, and nitrogen compounds, dictates the developmental programs and the growth rates of yeast cells. A number of overlapping signaling networks--those centered on Ras/protein kinase A, AMP-activated ...

    Abstract Availability of key nutrients, such as sugars, amino acids, and nitrogen compounds, dictates the developmental programs and the growth rates of yeast cells. A number of overlapping signaling networks--those centered on Ras/protein kinase A, AMP-activated kinase, and target of rapamycin complex I, for instance--inform cells on nutrient availability and influence the cells' transcriptional, translational, posttranslational, and metabolic profiles as well as their developmental decisions. Here I review our current understanding of the structures of the networks responsible for assessing the quantity and quality of carbon and nitrogen sources. I review how these signaling pathways impinge on transcriptional, metabolic, and developmental programs to optimize survival of cells under different environmental conditions. I highlight the profound knowledge we have gained on the structure of these signaling networks but also emphasize the limits of our current understanding of the dynamics of these signaling networks. Moreover, the conservation of these pathways has allowed us to extrapolate our finding with yeast to address issues of lifespan, cancer metabolism, and growth control in more complex organisms.
    MeSH term(s) Animals ; Carbon/metabolism ; Humans ; Nitrogen/metabolism ; Saccharomyces/growth & development ; Saccharomyces/metabolism
    Chemical Substances Carbon (7440-44-0) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2012-09-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1534/genetics.111.135731
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 767: Show issues Location:
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  9. Article ; Online: Infection diagnosis in hydrocephalus CT images: a domain enriched attention learning approach.

    Yu, Mingzhao / Peterson, Mallory R / Cherukuri, Venkateswararao / Hehnly, Christine / Mbabazi-Kabachelor, Edith / Mulondo, Ronnie / Nsubuga Kaaya, Brian / Broach, James R / Schiff, Steven J / Monga, Vishal

    Journal of neural engineering

    2023  Volume 20, Issue 3

    Abstract: ... ...

    Abstract Objective
    MeSH term(s) Child ; Humans ; Deep Learning ; Tomography, X-Ray Computed/methods ; Neural Networks, Computer ; Hydrocephalus/diagnostic imaging ; Attention
    Language English
    Publishing date 2023-06-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2170901-4
    ISSN 1741-2552 ; 1741-2560
    ISSN (online) 1741-2552
    ISSN 1741-2560
    DOI 10.1088/1741-2552/acd9ee
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6071: Show issues Location:
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  10. Article ; Online: Transcriptional Response of Multi-Stress-Tolerant Saccharomyces cerevisiae to Sequential Stresses

    Costa, Ane Catarine Tosi / Russo, Mariano / Fernandes, A. Alberto R. / Broach, James R. / Fernandes, Patricia M. B.

    Fermentation. 2023 Feb. 20, v. 9, no. 2

    2023  

    Abstract: During the fermentation process, yeast cells face different stresses, and their survival and fermentation efficiency depend on their adaptation to these challenging conditions. Yeast cells must tolerate not only a single stress but also multiple ... ...

    Abstract During the fermentation process, yeast cells face different stresses, and their survival and fermentation efficiency depend on their adaptation to these challenging conditions. Yeast cells must tolerate not only a single stress but also multiple simultaneous and sequential stresses. However, the adaptation and cellular response when cells are sequentially stressed are not completely understood. To explore this, we exposed a multi-stress-tolerant strain (BT0510) to different consecutive stresses to globally explore a common response, focusing on the genes induced in both stresses. Gene Ontology, pathway analyses, and common transcription factor motifs identified many processes linked to this common response. A metabolic shift to the pentose phosphate pathway, peroxisome activity, and the oxidative stress response were some of the processes found. The SYM1, STF2, and HSP genes and the transcription factors Adr1 and Usv1 may play a role in this response. This study presents a global view of the transcriptome of a multi-resistance yeast and provides new insights into the response to sequential stresses. The identified response genes can indicate future directions for the genetic engineering of yeast strains, which could improve many fermentation processes, such as those used for bioethanol production and beverages.
    Keywords Saccharomyces cerevisiae ; ethanol production ; fermentation ; gene ontology ; oxidative stress ; pentose phosphate cycle ; stress response ; transcription (genetics) ; transcription factors ; transcriptome ; yeasts
    Language English
    Dates of publication 2023-0220
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2813985-9
    ISSN 2311-5637
    ISSN 2311-5637
    DOI 10.3390/fermentation9020195
    Database NAL-Catalogue (AGRICOLA)

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