Nature Search

Erratum: Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy

Raul Perez-Jimenez
Jingyuan Li
Julio M Fernandez
Amendments and Corrections01 Dec 2009
Nature Structural & Molecular Biology

Volume: 16, P: 1331
Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

Here, the authors present Paraphase, a HiFi-based informatics method that resolves highly similar genes located in segmental duplications. They apply Paraphase to 316 paralogous genes and summarize extensive genetic diversity across populations.

Xiao Chen
Daniel Baker
Michael A. Eberle
ResearchOpen Access08 Mar 2025
Nature Communications

Volume: 16, P: 1-13
Genzyme acquires Cell Genesys

Eric Niiler
Research01 Dec 1999
Nature Biotechnology

Volume: 17, P: 1151-1152
The glycosylation design space for recombinant lysosomal replacement enzymes produced in CHO cells

Lysosomal replacement enzymes are taken up by cell surface receptors that recognize glycans, the effects of different glycan features are unknown. Here the authors present a gene engineering screen in CHO cells that allows custom N-glycan-decorated enzymes with improved circulation time and organ distribution.

Weihua Tian
Zilu Ye
Zhang Yang
ResearchOpen Access30 Apr 2019
Nature Communications

Volume: 10, P: 1-13
An experimental phylogeny to benchmark ancestral sequence reconstruction

Methods for ancestral sequence reconstruction are currently tested with computer simulations, since true biological phylogenies are unknown. Here, Randall et al.build an experimental phylogeny to benchmark the performance of alternate ancestral sequence reconstruction algorithms in inferring ancestral genotypes and phenotypes.

Ryan N. Randall
Caelan E. Radford
Eric A. Gaucher
ResearchOpen Access15 Sept 2016
Nature Communications

Volume: 7, P: 1-6
Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

Human disease genetics is extended to the identification of individuals who remain healthy despite carrying highly penetrant disease-causing mutations.

Rong Chen
Lisong Shi
Stephen H Friend
Research11 Apr 2016
Nature Biotechnology

Volume: 34, P: 531-538
Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy

Thioredoxins (Trxs) reduce disulfide bonds via a Michaelis-Menten mechanism. Upon substrate stretching at high forces, an S_N2 reaction can be used by bacterial Trxs. A third mechanism, single-electron transfer, is now revealed in Trxs of either bacterial or eukaryotic origin, and is correlated with the depth of the Trx substrate-binding groove.

Raul Perez-Jimenez
Jingyuan Li
Julio M Fernandez
Research13 Jul 2009
Nature Structural & Molecular Biology

Volume: 16, P: 890-896
Genome-wide association study of REM sleep behavior disorder identifies polygenic risk and brain expression effects

REM-sleep behavior disorder often precedes Parkinson’s disease or dementia. Here, the authors perform a genome-wide association study for REM-sleep behavior disorder, and discover how it potentially affects gene expression in the brain.

Lynne Krohn
Karl Heilbron
Ziv Gan-Or
ResearchOpen Access05 Dec 2022
Nature Communications

Volume: 13, P: 1-16
Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis

The trafficking defect associated with the cystic fibrosis disease-linked allele of the CFTR chloride channel is alleviated by inhibitors of histone deacetylases, suggesting that altering the transcription of genes associated with protein misfolding can ameliorate disease.

Darren M Hutt
David Herman
William E Balch
Research06 Dec 2009
Nature Chemical Biology

Volume: 6, P: 25-33
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

Eric A. Gaucher
J. Michael Thomson
Steven A. Benner
Research18 Sept 2003
Nature

Volume: 425, P: 285-288
An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals

Gabriel A. Lazarin
Imran S. Haque
Balaji S. Srinivasan
ResearchOpen Access13 Sept 2012
Genetics in Medicine

Volume: 15, P: 178-186
Expanded carrier screening in an infertile population: how often is clinical decision making affected?

Jason M. Franasiak
Meir Olcha
Richard T. Scott Jr
Research03 Mar 2016
Genetics in Medicine

Volume: 18, P: 1097-1101
Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago

Using phylogenetic analysis of a hopanoid-producing gene in bacteria, the authors establish fossil 2-methylhopanes as lipid biomarkers for aerobic cyanobacteria and reveal the role of cyanobacteria in primary production before 750 million years ago.

Yosuke Hoshino
Benjamin J. Nettersheim
Eric A. Gaucher
ResearchOpen Access26 Oct 2023
Nature Ecology & Evolution

Volume: 7, P: 2045-2054
Resurrecting ancestral alcohol dehydrogenases from yeast

J Michael Thomson
Eric A Gaucher
Steven A Benner
Research01 May 2005
Nature Genetics

Volume: 37, P: 630-635
Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction

The pharmaceutical properties of coagulation factor VIII are improved by reconstructing the protein's ancestral sequence.

Philip M Zakas
Harrison C Brown
Christopher B Doering
Research26 Sept 2016
Nature Biotechnology

Volume: 35, P: 35-37
Palaeotemperature trend for Precambrian life inferred from resurrected proteins

Using phylogeny to reconstruct proteins inferred to have existed in the ancestry of organisms is a powerful and provocative way to discover the evolutionary processes of life. A protein from various stages in the history of life has been reconstructed to show that life originated in a hot environment, and has tracked the cooling of Earth through time.

Eric A. Gaucher
Sridhar Govindarajan
Omjoy K. Ganesh
Research07 Feb 2008
Nature

Volume: 451, P: 704-707
Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.

Gloria Gamiz-Arco
Luis I. Gutierrez-Rus
Jose M. Sanchez-Ruiz
ResearchOpen Access15 Jan 2021
Nature Communications

Volume: 12, P: 1-16
Genomic insertion of ancestral uricase into human liver cells to determine metabolic consequences of pseudogenization

Lais de Lima Balico
Eric A. Gaucher
ResearchOpen Access18 Jul 2025
Scientific Reports

Volume: 15, P: 1-12
De novo active sites for resurrected Precambrian enzymes

The emergence of novel catalytic functions in ancient proteins likely played a role in the evolution of modern enzymes. Here, the authors use protein sequences from Precambrian beta-lactamases and demonstrate that a single hydrophobic-to-ionizable amino acid mutation can lead to substantial Kemp eliminase activity.

Valeria A. Risso
Sergio Martinez-Rodriguez
Jose M. Sanchez-Ruiz
ResearchOpen Access18 Jul 2017
Nature Communications

Volume: 8, P: 1-13
Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

Using phylogenetic analysis, ancestral forms of thioredoxin reflecting the sequences likely to have existed at key evolutionary points have now been synthesized and analyzed. Single-molecule analysis indicates that all of the reconstructed enzymes use the extant reaction mechanism but that the most ancient are optimally active at low pH and resistant to higher temperatures, conditions that would have existed on early earth.

Raul Perez-Jimenez
Alvaro Inglés-Prieto
Julio M Fernandez
Research03 Apr 2011
Nature Structural & Molecular Biology

Volume: 18, P: 592-596
Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA

Huiwen Che
Darine Villela
Joris Robert Vermeesch
Research06 Feb 2020
Genetics in Medicine

Volume: 22, P: 962-973
Expanding the limits of the second genetic code with ribozymes

Flexizymes have been used to expand the scope of chemical substrates for ribosome-directed polymerization in vitro. Here the authors deduce design rules of Flexizyme-mediated tRNA acylation that more effectively predict the incorporation of new monomers into peptides.

Joongoo Lee
Kenneth E. Schwieter
Michael C. Jewett
ResearchOpen Access08 Nov 2019
Nature Communications

Volume: 10, P: 1-12
Life, death and autophagy

In this Review, Doherty and Baehrecke discuss the multiple roles of autophagy during cell survival and cell death. They cover the interplay between autophagy, apoptosis and necrosis, as well as engulfment and inflammation.

Johnna Doherty
Eric H. Baehrecke
Reviews17 Sept 2018
Nature Cell Biology

Volume: 20, P: 1110-1117
Progranulin, lysosomal regulation and neurodegenerative disease

Recent studies suggest that progranulin has an important role in lysosome biogenesis and innate immunity in the brain. In this Progress article, Kao and colleagues suggest that progranulin also plays a part in suppressing excessive neuroinflammation during ageing.

Aimee W. Kao
Andrew McKay
Eric J. Huang
Reviews24 Apr 2017
Nature Reviews Neuroscience

Volume: 18, P: 325-333
Gene expression differences associated with alcohol use disorder in human brain

Caryn Willis
Julie D. White
Dana B. Hancock
ResearchOpen Access12 Oct 2024
Molecular Psychiatry

Volume: 30, P: 1617-1626
Progress and Prospects: Gene Therapy Clinical Trials (Part 1)

Eric Alton
Reviews02 Oct 2007
Gene Therapy

Volume: 14, P: 1439-1447
Repurposing drugs to treat cardiovascular disease in the era of precision medicine

Drugs can be repurposed for new therapeutic indications. In this Review, Mercola and colleagues summarize the latest techniques for systematic drug repurposing and re-engineering, which could increase the pace, efficiency and cost-effectiveness of drug discovery for the treatment of cardiovascular disease.

Mena Abdelsayed
Eric J. Kort
Mark Mercola
Reviews23 May 2022
Nature Reviews Cardiology

Volume: 19, P: 751-764
Lysosomal and network alterations in human mucopolysaccharidosis type VII iPSC-derived neurons

Neus Bayó-Puxan
Ana Paula Terrasso
Eric J. Kremer
ResearchOpen Access09 Nov 2018
Scientific Reports

Volume: 8, P: 1-19
Frequency of diagnostic errors in the neonatal intensive care unit: a retrospective cohort study

Grant J. Shafer
Hardeep Singh
Kanekal Suresh Gautham
Research04 Mar 2022
Journal of Perinatology

Volume: 42, P: 1312-1318
Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4B

Kelly L. Warfield
Kaitlyn R. Schaaf
Suman R. Das
ResearchOpen Access16 May 2019
Scientific Reports

Volume: 9, P: 1-13
Thermodynamic evidence of giant salt deposit formation by serpentinization: an alternative mechanism to solar evaporation

Mathieu Debure
Arnault Lassin
Eric C. Gaucher
ResearchOpen Access12 Aug 2019
Scientific Reports

Volume: 9, P: 1-11
Intravascular bone marrow accumulation in persistent polyclonal lymphocytosis: a misleading feature for B-cell neoplasm

Pierre Feugier
Anne Kennel de March
Eric Labouyrie
Research14 May 2004
Modern Pathology

Volume: 17, P: 1087-1096
Systematic design and comparison of expanded carrier screening panels

Kyle A Beauchamp
Dale Muzzey
Imran S Haque
ResearchOpen Access22 Jun 2017
Genetics in Medicine

Volume: 20, P: 55-63
Molecular diagnostic experience of whole-exome sequencing in adult patients

Jennifer E. Posey
Jill A. Rosenfeld
Sharon E. Plon
Research03 Dec 2015
Genetics in Medicine

Volume: 18, P: 678-685

Search

Erratum: Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

Genzyme acquires Cell Genesys

The glycosylation design space for recombinant lysosomal replacement enzymes produced in CHO cells

An experimental phylogeny to benchmark ancestral sequence reconstruction

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy

Genome-wide association study of REM sleep behavior disorder identifies polygenic risk and brain expression effects

Reduced histone deacetylase 7 activity restores function to misfolded CFTR in cystic fibrosis

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals

Expanded carrier screening in an infertile population: how often is clinical decision making affected?

Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago

Resurrecting ancestral alcohol dehydrogenases from yeast

Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction

Palaeotemperature trend for Precambrian life inferred from resurrected proteins

Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

Genomic insertion of ancestral uricase into human liver cells to determine metabolic consequences of pseudogenization

De novo active sites for resurrected Precambrian enzymes

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA

Expanding the limits of the second genetic code with ribozymes

Life, death and autophagy

Progranulin, lysosomal regulation and neurodegenerative disease

Gene expression differences associated with alcohol use disorder in human brain

Progress and Prospects: Gene Therapy Clinical Trials (Part 1)

Repurposing drugs to treat cardiovascular disease in the era of precision medicine

Lysosomal and network alterations in human mucopolysaccharidosis type VII iPSC-derived neurons

Frequency of diagnostic errors in the neonatal intensive care unit: a retrospective cohort study

Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4B

Thermodynamic evidence of giant salt deposit formation by serpentinization: an alternative mechanism to solar evaporation

Intravascular bone marrow accumulation in persistent polyclonal lymphocytosis: a misleading feature for B-cell neoplasm

Systematic design and comparison of expanded carrier screening panels

Molecular diagnostic experience of whole-exome sequencing in adult patients

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