Editorial Material
Biochemistry & Molecular Biology
Verena J. Schuenemann
Summary: Ancient DNA methodologies have the potential to study the past prevalence and evolutionary history of pathogens. A recent study identified bacteria that cause plague and typhoid fever in Minoan Crete, illustrating both the possibilities and limitations of ancient pathogen genomics.
Article
Immunology
Junyan Jin, Liting Xiao, Yarong Wu, Zhulin Sun, Ziyao Xiong, Yanbing Li, Yanting Zhao, Wenwu Yao, Leiming Shen, Yiming Cui, Yafang Tan, Yanping Han, Zongmin Du, Yujun Cui, Ruifu Yang, Kai Song, Yajun Song
Summary: This study revealed the frequent mutations in the YPO0623 gene of Yersinia pestis and their potential association with natural selection. The deletion of YPO0623 enhanced the growth and stress tolerance of Y. pestis. Additionally, the deletion of YPO0623 resulted in the upregulation of genes associated with the type VI secretion system (T6SS), which may play a crucial role in Y. pestis' response to environmental fluctuations.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jennifer Klunk, Tauras P. Vilgalys, Christian E. Demeure, Xiaoheng Cheng, Mari Shiratori, Julien Madej, Remi Beau, Derek Elli, Maria Patino, Rebecca Redfern, Sharon N. DeWitte, Julia A. Gamble, Jesper L. Boldsen, Ann Carmichael, Nukhet Varlik, Katherine Eaton, Jean-Christophe Grenier, G. Brian Golding, Alison Devault, Jean-Marie Rouillard, Vania Yotova, Renata Sindeaux, Chun Jimmie Ye, Matin Bikaran, Anne Dumaine, Jessica F. Brinkworth, Dominique Missiakas, Guy A. Rouleau, Matthias Steinrucken, Javier Pizarro-Cerda, Hendrik N. Poinar, Luis B. Barreiro
Summary: Infectious diseases have been a significant driving force in human evolution. The second pandemic of plague, known as the Black Death, caused by the bacterium Yersinia pestis, resulted in a devastating mortality event in Afro-Eurasia. By studying genetic variation in immune-related genes, researchers found evidence of positive selection during the Black Death. Several variants associated with immune response and control of Yersinia pestis were identified. Furthermore, protective variants overlapped with alleles associated with increased susceptibility to autoimmune diseases.
Article
Multidisciplinary Sciences
Maria A. Spyrou, Lyazzat Musralina, Guido A. Gnecchi Ruscone, Arthur Kocher, Pier-Giorgio Borbone, Valeri Khartanovich, Alexandra Buzhilova, Leyla Djansugurova, Kirsten Bos, Denise Kuhnert, Wolfgang Haak, Philip Slavin, Johannes Krause
Summary: This study reports ancient DNA data from cemeteries in Kyrgyzstan, providing evidence for the involvement of Yersinia pestis in the medieval Black Death pandemic and supporting a local emergence of the recovered ancient strain.
Article
Biotechnology & Applied Microbiology
Igor Vasconcelos Rocha, Carlos Alberto Neves Andrade, Marise Sobreira, Nilma Cintra Leal, Alzira Maria Paiva Almeida, Matheus Filgueira Bezerra
Summary: We developed a new selective LB-based medium called CYP broth for recovering stored Y. pestis subcultures and isolating Y. pestis strains for Plague surveillance. The CYP broth inhibited contaminating microorganisms and enriched Y. pestis growth through iron supplementation. It also successfully isolated other pathogenic Yersinia species.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Fan Liu, Yi Shi, Yakun Fang, Zhenshan Liu, Yu Xin, Zhenghua Gu, Zitao Guo, Liang Zhang
Summary: In this study, a potential enzyme sequence with the function of carnosine synthesis was screened out using the ASR technique. The enzymatic properties of the enzyme LUCA-DmpA were characterized, including its melting temperature, denaturation enthalpy, and secondary structure composition. The enzyme exhibited optimal temperature and pH, as well as remarkable pH tolerance and promotion of activity by organic solvents. These findings demonstrate the potential of LUCA-DmpA for industrial applications.
Article
Biochemistry & Molecular Biology
Mohamad Farihan Afnan Mohd Rozi, Raja Noor Zaliha Raja Abd Rahman, Adam Thean Chor Leow, Mohd Shukuri Mohamad Ali
Summary: This study investigates the evolutionary process of bacterial lipases from family I.3 and reconstructs the last universal common ancestor (LUCA) sequence through phylogenetic tree inference and ancestral sequence reconstruction (ASR) technique. The purified LUCA exhibits high temperature and pH adaptability, as well as tolerance towards metal ions and organic solvents. The findings contribute to the understanding of temperature and environment during ancient times, and the reconstructed ancestral enzymes have improved properties for industrial applications using ASR technique as a general enzyme engineering technique.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Sarah Z. Dungan, Belinda S. W. Chang
Summary: This study reconstructs and experiments on the light-activation metrics of rhodopsin pigments in the eyes of cetaceans, revealing significant changes in their visual system during the evolution from terrestrial to aquatic environments. The findings show a blue-shift in the spectral sensitivity of cetaceans' vision and an increased decay rate of light-activated rhodopsin. These transitions may be related to cetaceans' adaptation to deep-diving underwater environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Toni De-Dios, Pablo Carrion, Inigo Olalde, Laia Llovera Nadal, Esther Lizano, Didac Pamies, Tomas Marques-Bonet, Francois Balloux, Lucy van Dorp, Carles Lalueza-Fox
Summary: Ancient pathogen genomics is a growing field that reconstructs past epidemics, suggesting that Europeans may have introduced deadly paratyphoid fever to post-contact American populations. Despite proposed plague epidemics, genome-wide data from two Spanish soldiers besieging Barcelona in 1652 did not show evidence of plague infection, but did reveal substantial presence of the Salmonella enterica serovar Paratyphi C lineage, linking to paratyphoid fever in colonial Mexico. This supports the idea that Paratyphi C enteric fever was more common in Europe and the Americas in the past.
Article
Microbiology
Lihua Yang, Jing Wang, Shuguang Lu, Youhong Zhong, Kun Xiong, Xiaoxiao Liu, Bing Liu, Xiaoxue Wang, Peng Wang, Shuai Le
Summary: This study discovered a carrier state bacterial phage coexistence mediated by H-NS, which promotes long-term coexistence of host bacteria and phages in the soil. This finding challenges the conventional lytic-lysogenic binary model and demonstrates the ubiquity and ecological importance of the carrier state in nature.
Article
Biology
Joanna H. Bonczarowska, Julian Susat, Ben Krause-Kyora, Dorthe Dangvard Pedersen, Jesper Boldsen, Lars Agersnap Larsen, Lone Seeberg, Almut Nebel, Daniel Unterweger
Summary: By analyzing ancient and modern strains of Yersinia pestis, researchers have identified a phage that is exclusively present in modern strains and may have contributed to the virulence of the Modern pandemic.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
George S. Long, Jennifer Klunk, Ana T. Duggan, Madeline Tapson, Valentina Giuffra, Lavinia Gazze, Antonio Fornaciari, Sebastian Duchene, Gino Fornaciari, Olivier Clermont, Erick Denamur, G. Brian Golding, Hendrik Poinar
Summary: This study reconstructed the ancient Escherichia coli genome from a 16th-century gallstone found in an Italian mummy. The ancient E. coli strain belonged to phylogroup A and had an exceptionally rare sequence type 4995. However, no pathovar specific genes or acquired antibiotic resistances were identified. This research provides insight into the burden of opportunistic E. coli infections in the past.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Analytical
Feng-Ping Lin, Hui-Ling Hsu, Pei-Yi Tsui, Chung-Chih Liang, Chien-Hsing Lu, Jem-Kun Chen
Summary: A simple method for detecting pathogens in human blood specimens quickly at the point of care was developed to prevent the widespread transmission of communicable diseases, with Yersinia pestis as the first target. The system achieved high sensitivity and specificity, based on one-dimensional diffraction grating (ODG) chips and laser beams. It was portable and could complete the entire process within minutes at the point of care.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemistry & Molecular Biology
Da Di, Jeanne Simon Thomas, Mathias Currat, Jose Manuel Nunes, Alicia Sanchez-Mazas
Summary: In this study, DNA was extracted from medieval plague victims and compared to modern populations to investigate changes in human leukocyte antigen (HLA) genotypes. The authors found significant differences in HLA frequencies between ancient and modern populations, suggesting a long-term effect of Yersinia pestis on human immunity genes. However, further analyses and simulations did not support these conclusions, indicating that ancient DNA may not provide sufficient evidence for HLA protection or susceptibility to plague.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Virology
Mikael Skurnik, Salla Jaakkola, Laura Mattinen, Lotta von Ossowski, Ayesha Nawaz, Maria Pajunen, Lotta J. Happonen
Summary: This study describes the isolation of two bacteriophages from sewage water samples in Turku, Finland. These phages are a novel type of dwarf myovirus and a T4-like myovirus, with different host ranges including Yersinia pestis and other Enterobacterales. The genomes, proteomes, and life cycles of these Yersinia myoviruses, fEV-1 and fD1, were examined.
Article
Biochemistry & Molecular Biology
Mathieu Groussin, Bastien Boussau, Gergely Szoellosi, Laura Eme, Manolo Gouy, Celine Brochier-Armanet, Vincent Daubin
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Article
Biology
Gergely J. Szoellosi, Adrian Arellano Davin, Eric Tannier, Vincent Daubin, Bastien Boussau
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2015)
Article
Genetics & Heredity
Florent Lassalle, Severine Perian, Thomas Bataillon, Xavier Nesme, Laurent Duret, Vincent Daubin
Article
Cell Biology
Vincent Daubin, Gergely J. Szoellosi
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2016)
Article
Evolutionary Biology
Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Severine Berard, Cedric Chauve, Celine Scornavacca, Vincent Daubin, Eric Tannier
GENOME BIOLOGY AND EVOLUTION
(2017)
Article
Biochemistry & Molecular Biology
Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biemont, Vincent Daubin, Cedric Feschotte, Dominique Pontier
Article
Biochemical Research Methods
Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perriere
BMC BIOINFORMATICS
(2013)
Article
Biochemical Research Methods
Murray Patterson, Gergely Szoellosi, Vincent Daubin, Eric Tannier
BMC BIOINFORMATICS
(2013)
Article
Biotechnology & Applied Microbiology
Subarna Thakur, Philippe Normand, Vincent Daubin, Louis S. Tisa, Arnab Sen
Article
Microbiology
Arnab Sen, Vincent Daubin, Danis Abrouk, Isaac Gifford, Alison M. Berry, Philippe Normand
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Martha H. Ramirez-Bahena, Ludovic Vial, Florent Lassalle, Benjamin Diel, David Chapulliot, Vincent Daubin, Xavier Nesme, Daniel Muller
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2014)
Article
Biochemistry & Molecular Biology
Hemalatha Golaconda Ramulu, Mathieu Groussin, Emmanuel Talla, Remi Planel, Vincent Daubin, Celine Brochier-Armanet
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2014)
Review
Microbiology
Berenice Batut, Carole Knibbe, Gabriel Marais, Vincent Daubin
NATURE REVIEWS MICROBIOLOGY
(2014)
Article
Evolutionary Biology
Joel Sjostrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad, Jens Lagergren
SYSTEMATIC BIOLOGY
(2014)