Article
Biochemistry & Molecular Biology
Sylwia Gorka, Dawid Kubiak, Malgorzata Ciesinska, Katarzyna Niedojadlo, Jaroslaw Tyburski, Janusz Niedojadlo
Summary: Retention of RNA in the nucleus is crucial for regulating translation and controlling mRNA levels variability. The function of Cajal bodies (CBs) in RNA accumulation in the nuclei during stress depends on the plant organ. Intron retention is more important than CBs for RNA accumulation, as it allows mRNA to escape degradation and be translated in the cytoplasm. However, the absence of CBs leads to worse response to long hypoxia stress in A. thaliana.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Yunying Cheng, Jinlin Chen, Irum Mukhtar, Jianming Chen
Summary: The research identified an extensive expansion of the nuclear receptor family in the marine free-living flatworm Macrostomum lignano. Duplicated NR pairs and NR orthologs in flatworms all experienced purifying selection. The presence of NR3-like genes in Macrostomum lignano was first reported in flatworms.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Dumitrana Iordache, Gabriela-Maria Baci, Oana Caprita, Anca Farkas, Andreea Lup, Anca Butiuc-Keul
Summary: CRISPR-Cas is an adaptive immunity system of prokaryotes, consisting of CRISPR arrays and associated proteins. The study aimed to establish correlations between enterobacterial CRISPR loci, sequence of direct repeats, number of spacer units, geographical origin, and collection source. Analysis of 3474 genomes from Salmonella enterica, Escherichia coli, and Klebsiella pneumoniae showed that the most prevalent system was I-E in all three taxa, with E. coli also presenting the I-F type.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Maxime Mazille, Katarzyna Buczak, Peter Scheiffele, Oriane Mauger
Summary: The nuclear envelope not only acts as a physical barrier between the nucleus and cytosol, but also plays a role in regulating gene expression. This study reveals that a majority of stable intron-retaining mRNAs are retained in the nucleus in mature mouse cortical neurons. Upon neuronal stimulation, some transcripts undergo degradation while others complete splicing and are exported to the cytosol, leading to rapid increases in protein levels. Different forms of stimulation mobilize distinct groups of intron-retaining transcripts, with selectivity arising from specific signaling pathways.
Article
Biochemistry & Molecular Biology
Scott J. Steppan, Anna A. Meyer, Lisa N. Barrow, Bader H. Alhajeri, Amani S. Y. M. Al-Zaidan, Paul M. Gignac, Gregory Erickson
Summary: The initial conquest of land by vertebrates allowed access to new resources and led to a major diversification. However, little is known about the phylogenetic relationships and ecological stages in this transition. Mudskippers, a type of actinopterygians, are highly terrestrial and well-studied, making them good analogs for studying the initial conquest of land. Through molecular analysis, researchers found evidence for two independent terrestrial transitions and a complex range of ecological and morphological forms. Contrary to earlier studies, they did not find support for a linear model of locomotory transition from aquatic to terrestrial. This study highlights the importance of mudskippers in understanding the evolution of land conquest.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Yuta Kinoshita, Hidekazu Niwa, Eri Uchida-Fujii, Toshio Nukada
Summary: A method using long amplicon sequencing targeting the rRNA operon provides higher taxonomic resolution for microbial communities, with over 90% accuracy at species level and performance similar to shotgun sequencing in equine fecal samples. However, it may underestimate the compositional percentages of certain bacterial strains, although the overall results are minimally affected.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Amandine Duchemin, Tina O'Grady, Sarah Hanache, Agnes Mereau, Marc Thiry, Ludivine Wacheul, Catherine Michaux, Eric Perpete, Eric Hervouet, Paul Peixoto, Felix G. M. Ernst, Yann Audic, Franck Dequiedt, Denis L. J. Lafontaine, Denis Mottet
Summary: TFIP11, a human homolog of the yeast spliceosome disassembly factor Ntr1, is essential for U6 snRNA 2'-O-methylation and U4/U6.U5 tri-snRNP assembly, independently of its known partner DHX15. This reveals a previously unrecognized function of TFIP11 in spliceosome assembly regulation in human cells.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Thomas W. Dudgeon, Marissa C. H. Livius, Noel Alfonso, Stephanie Tessier, Jordan C. Mallon
Summary: A new model using intramanual measurements has been introduced to estimate habitat likelihood more accurately. This model supports the hypothesis that stem-turtles were primarily terrestrial in nature.
ECOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Tsuyoshi Tanaka, Yoshiaki Maeda, Noraiza Suhaimi, Chiharu Tsuneoka, Tomomi Nonoyama, Tomoko Yoshino, Naohiro Kato, Kyle J. Lauersen
Summary: The study found the phenomenon of intron mediated enhancement (IME) in the oleaginous diatom, Fistulifera solaris, showing that inclusion of introns in heterologous sequences can significantly increase transgene expression, leading to enhanced resistance and selection.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Chun Shen Lim, Brooke N. Weinstein, Scott W. Roy, Chris M. Brown
Summary: This study used fungal genomes to address questions related to intron evolution, revealing a complex evolutionary history of fungal introns and their underappreciated roles in gene expression. The research showed that intron reduction has occurred in various clades, with some fungi containing as few as zero to 7.6 introns per 1 kb of protein-coding sequence. The study also found conserved introns in ribosome-associated genes, highlighting their potential importance in ribosome biogenesis and gene expression coordination.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Cell Biology
Jigeesha Mukhopadhyay, Georg Hausner
Summary: Introns in organellar genomes play important roles in encoding proteins and participating in non-canonical splicing. Different types of introns show diverse distribution patterns in fungi, plants, and algae.
Editorial Material
Biochemistry & Molecular Biology
Michael A. Kiebler, Jovica Ninkovic
Summary: A recent study reveals the presence of cytoplasmic RNA granules containing spliceosome protein SNRNP70 in zebrafish motoneurons. Interestingly, cytoplasmic SNRNP70 plays a crucial role in functional neuromuscular junctions, possibly by regulating alternative splicing of z+agrin mRNA.
Article
Environmental Sciences
Juliana dos Santos Mendonca, Julio Cesar Neves de Almeida, Lucelia Goncalves Vieira, Liria Queiroz Luz Hirano, Andre Luiz Quagliatto Santos, Denis Vieira Andrade, Guilherme Malafaia, Robson Jose de Oliveira Jr, Marcelo Emilio Beletti
Summary: Pesticides, especially glyphosate and fipronil, have mutagenic and toxic effects on neonates of Podocnemis expansa, causing histopathological damage and genetic alterations. The presence of blebbed nuclei, moved nuclei, and notched nuclei indicate the increased frequency of erythrocyte nuclear abnormalities. Exposure to fipronil leads to congestion and inflammatory infiltrate in the liver tissue and congestion and necrosis in the encephalon. This study highlights the significance of using different biomarkers to evaluate the ecotoxicological effects of pesticides on oviparous animals.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Eduardo Ascarrunz, Julien Claude, Walter G. Joyce
Summary: Quantitative analyses examining the placement of Messel geoemydids in a reference tree generated from molecular data show that their position remains uncertain, with different methods yielding varied results. Parsimony suggests placement as sister to two different species, but with weak support, highlighting the challenge of determining the relationships within this group.
Article
Biochemical Research Methods
Soren M. Karst, Ryan M. Ziels, Rasmus H. Kirkegaard, Emil A. Sorensen, Daniel McDonald, Qiyun Zhu, Rob Knight, Mads Albertsen
Summary: High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, a new approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies (ONT) or Pacific Biosciences circular consensus sequencing was reported, achieving high-accuracy single-molecule consensus sequences. The method was successfully applied to sequence ribosomal RNA operon amplicons and genomic sequences of microbial communities, showing a very low chimera rate.
Article
Biodiversity Conservation
Caroline M. Dong, Tag N. Engstrom, Robert C. Thomson
CONSERVATION GENETICS
(2016)
Review
Biochemistry & Molecular Biology
Anthony J. Barley, Patrick J. Monnahan, Robert C. Thomson, L. Lee Grismer, Rafe M. Brown
Article
Biochemistry & Molecular Biology
Anthony J. Barley, Robert C. Thomson
Article
Biochemistry & Molecular Biology
Catherine E. Newman, Christopher C. Austin
Article
Biochemistry & Molecular Biology
Phillip Q. Spinks, Robert C. Thomson, Evan McCartney-Melstad, H. Bradley Shaffer
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2016)
Article
Evolutionary Biology
Jeremy M. Brown, Robert C. Thomson
SYSTEMATIC BIOLOGY
(2017)
Article
Biotechnology & Applied Microbiology
Catherine E. Newman, T. Ryan Gregory, Christopher C. Austin
Article
Evolutionary Biology
Kenneth L. Krysko, Leroy P. Nunez, Catherine E. Newman, Brian W. Bowen
JOURNAL OF HEREDITY
(2017)
Article
Biochemistry & Molecular Biology
Adrian Nieto-Montes de Oca, Anthony J. Barley, Rubi N. Meza-Lazaro, Uri O. Garcia-Vazquez, Joan G. Zamora-Abrego, Robert C. Thomson, Adam D. Leache
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2017)
Article
Evolutionary Biology
Anthony J. Barley, Jeremy M. Brown, Robert C. Thomson
SYSTEMATIC BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Robert C. Thomson, Phillip Q. Spinks, H. Bradley Shaffer
Summary: Living turtles exhibit extremely low species diversity despite their long evolutionary history, with climate and biogeography playing important roles in shaping their diversity. A study analyzing a large molecular dataset of turtles found that a threefold increase in diversification was associated with the emergence of new continental margins during the Eocene-Oligocene transition, driven by global cooling and drying. This shift in environmental conditions led to both regional extinctions and a burst of speciation in newly exposed habitats.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Anthony J. Barley, James E. Cordes, James M. Walker, Robert C. Thomson
Summary: Unisexual vertebrates typically form through hybridization events between sexual species, which can have important ecological consequences. Studying the genetic diversity in unisexual lineages has proven challenging, especially in understanding the contribution of historical hybridization events versus post formational mutation. This study on a diploid unisexual lizard species in Texas and Mexico highlights the genetic variation and historical patterns of hybridization, providing insights into the mechanisms that generate and maintain lineage diversity in unisexual species.
Article
Evolutionary Biology
Robert C. Thomson, Jeremy M. Brown
Summary: The growing scale of data sets has provided researchers with a wealth of information for inferring evolutionary history. However, standard approaches to assessing confidence in those inferences are outdated and cannot handle the challenges posed by modern genomic data. New methods are needed to evaluate the confidence and uncertainty in data sets.
SYSTEMATIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Anthony J. Barley, Adrian Nieto-Montes De Oca, Norma L. Manriquez-Moran, Robert C. Thomson
Summary: This study estimated an evolutionary network for a group of unisexual vertebrates and found that rates of gene introgression between species decrease with time since divergence. It also revealed that a threshold level of evolutionary divergence must be reached for hybridization to result in unisexuality, and hybridization rates can predict patterns of genetic diversity in whiptail lizards.
Article
Biodiversity Conservation
Catherine E. Newman
SOUTHEASTERN NATURALIST
(2017)