Evidence map›Paper›PMID 37746117›Full record

ArticleFrontiers in fungal biology2023

High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi.

Jennifer L Brown, Taylor Gierke, Lazarina V Butkovich, Candice L Swift, Vasanth Singan, Christopher Daum, Kerrie Barry, Igor V Grigoriev, Michelle A O'Malley

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in fungal biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.5field-weighted citation impact, top 39% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 5 citations in OpenAlex.

  1. Review
  2. Review
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 4 institutions in 1 country.

Jennifer L BrownDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States.
Taylor GierkeDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States.
Lazarina V ButkovichDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States.
Candice L SwiftDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States.
Vasanth SinganUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Christopher DaumUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Kerrie BarryUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Igor V GrigorievUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Michelle A O'MalleyDepartment of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States.
University of California, Santa Barbara · USLawrence Berkeley National Laboratory · USJoint BioEnergy Institute · USJoint Genome Institute · US

Funding

MARC at the University of California Santa BarbaraT34GM136466 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI Arica Ayalah Lubin, Joel H. Rothman · 2020 to 2026
$2.7M
NIGMS NIH HHS T34 GM136466
6 · The paper itself

Abstract

Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain

Indexed as

anaerobicCAZymesfungimethanogensRNA

Identifiers

PMID37746117
PMCPMC10512310
OpenAlexW4384523154

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.