Article
Multidisciplinary Sciences
Helena Massana-Cid, Claudio Maggi, Giacomo Frangipane, Roberto Di Leonardo
Summary: Optical feedback can be used to confine and gather bacteria, forming dense high-activity regions. This method is general and scalable, making it versatile for microengineering applications and studying non-equilibrium phenomena in active systems.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Yajing Song, Zhen Zhou, Jing Gu, Junmei Yang, Jiaoyu Deng
Summary: This study revealed that the resistance of E. coli to trimethoprim (TMP) is associated with the deletion of genes related to glutathione metabolism, leading to activation of drug resistance mechanisms when reducing the periplasmic glutathione content in E. coli.
MICROBIOLOGY SPECTRUM
(2021)
Review
Microbiology
Adrianna Aleksandrowicz, Muhammad Moman Khan, Katarzyna Sidorczuk, Mateusz Noszka, Rafal Kolenda
Summary: APEC, a common pathogen in poultry, relies on various adhesins to evade host defense mechanisms and cause infection. Understanding these adhesins is essential for developing effective strategies to combat APEC infections.
VETERINARY MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
A. Launay, C. -J. Wu, A. Dulanto Chiang, J. -H. Youn, P. P. Khil, J. P. Dekker
Summary: In this study, the authors utilized whole genome sequencing to characterize the adaptive evolution mechanisms of Bordetella hinzii in a patient with interleukin-12 receptor beta 1 deficiency. Results suggest that the inactivation of DNA proofreading activity in combination with the underlying host immunodeficiency facilitated rapid genomic adaptation of the pathogen. This highlights the fundamental role of host immune phenotype in shaping pathogen evolution following zoonotic infection.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Haoran Li, Yubo Wang, Yaohua Li, Wei Wang
Summary: The new method successfully quantifies bacterial viability at a single-cell level using optical tweezers, holding potential in antibiotic susceptibility testing, drug screening, and rapid diagnostics.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Haoran Li, Yubo Wang, Yaohua Li, Wei Wang
Summary: This study presents a new label-free bacterial viability assay based on optical tweezers technology, which quantifies bacterial viability by monitoring bacterial nanomotion in the optical traps. The assay is characterized by short time consumption, simple sample preparations, and no cytotoxicity, making it a reliable method for assessing bacterial viability at the single-cell level.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Ningyun Cai, Jiuzhou Chen, Ning Gao, Xiaomeng Ni, Yu Lei, Wei Pu, Lixian Wang, Bin Che, Liwen Fan, Wenjuan Zhou, Jinhui Feng, Yu Wang, Ping Zheng, Jibin Sun
Summary: In this study, the DNA replication and repair machinery of C. glutamicum were targeted. It was found that the PHP domain of DnaE1 played a key role in proofreading, and certain PHP variants increased the spontaneous mutation rate. Repression of the NucS-mediated post-replicative mismatch repair pathway or overexpression of newly screened NucS variants also affected DNA replication fidelity. Simultaneous interference with the DNA replication and repair machinery generated a binary genetic mutator that increased the mutation rate by up to 2352-fold. This study provides efficient tools for evolutionary engineering of C. glutamicum and may inspire the development of mutagenesis strategies for other microbial hosts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Vadim Dubinsky, Iris Dotan, Uri Gophna
Summary: We reconstructed bacterial genomes from specific sites within the human intestines and found that strains at these sites are genetically distinct yet interrelated and derived from a single founder population. Organ-specific metagenomic information can provide valuable insights into gastrointestinal diseases, such as inflammatory bowel disease. This study used metagenomic data obtained from colonoscopy aspirates to reconstruct the genomes of common gut bacteria and revealed site-specific evolution as well as the absence of site-specific adaptations in accessory genes.
Article
Biotechnology & Applied Microbiology
Jie Chen, Hao Yang, Yanru Feng, Qiuxiao Shi, Zhao Li, Ze Tao, Jie Fan, Youmei Jin, Shengfu Li, Jingqiu Cheng, Xiaofeng Lu
Summary: Researchers found that increasing the expression of NGR-TNFα from the original lower level by approximately 100 times could provide a new direction for the development of novel tumor-homing TNFα variants. Through a single nucleotide mutation and substitution of valine for leucine, the expression level of NGR-TNFα was successfully enhanced. The study results suggest that this amino acid substitution has minimal impact on the receptor binding, cytotoxicity, and antitumor effect of NGR-TNFα.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Miray Tonk, James J. Valdes, Alejandro Cabezas-Cruz, Andreas Vilcinskas
Summary: Arthropod antimicrobial peptides (AMPs) provide a potential source for new antibiotics with potent activity against multidrug-resistant bacterial pathogens. Synergistic effects can be achieved by combining AMPs from different sources. Hybrid peptides linked by glycine spacers show enhanced antibacterial activity, but can also exhibit increased cytotoxic activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Akos Vegvari, Xuepei Zhang, Roman A. Zubarev
Summary: This study successfully detected proteins from individual Escherichia coli bacteria for the first time, with validation of the findings through comparison with other samples and bulk proteomics data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Nicola Pellicciotta, Matteo Paoluzzi, Dario Buonomo, Giacomo Frangipane, Luca Angelani, Roberto Di Leonardo
Summary: By modulating bacterial motility with light, researchers have found a way to control the transport direction and speed of microscopic particles by adjusting the active pressure gradients. This discovery provides new insights into the potential use of active pressure for controlled transport of microscopic objects.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Vladimir Baytshtok, Xue Fei, Tsai-Ting Shih, Robert A. Grant, Justin C. Santos, Tania A. Baker, Robert T. Sauer
Summary: At low temperatures, protein degradation by the AAA+ HslUV protease is slow due to residues in the intermediate domain of the HslU(6) unfoldase blocking the axial channel, preventing substrate binding and degradation until heat-induced melting of this autoinhibitory plug activates HslUV proteolysis through a model supported by biochemical experiments with wild-type and mutant enzymes.
Article
Biochemistry & Molecular Biology
Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama
Summary: This study describes the unwinding mechanisms of the DUE in the replication origin oriC of Escherichia coli, which are promoted by DnaA, IHF, and the structural homolog HU. IHF and HU promote DUE unwinding by promoting the binding of R1/R5M-bound DnaAs to ssDUE. Notably, HU binds the R1-R5M interspace stimulated by ATP-DnaA and ssDUE, suggesting a model of DUE unwinding triggered by DnaA interactions and stabilized by HU binding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jae-Won Hyun, Kibin Lee, Ji-Hun Kim, Dae-Won Sim, Kyu-Tae Byun, Seung-Jae Jung, Jin Chul Paeng, Tae-Bong Kang, Jooho Park, Chan-Gil Kim, Hyung-Sik Won
Summary: The study demonstrates a method for extracellular production of anti-HER2 in Escherichia coli via nonpeptide-guided secretion, enabling purification of the intact protein with high affinity and dissociation constant for potential therapeutic or diagnostic applications in cancer.
PROCESS BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Yutaro Maeda, Ryo Mizuuchi, Shuji Shigenobu, Atsushi Shibai, Hazuki Kotani, Chikara Furusawa, Norikazu Ichihashi
Summary: By analyzing RNA genotypes, it has been found that there is a correlation between the structural fluctuation of RNA and adaptive evolution. RNA with smaller structural fluctuations tends to have higher fitness, and RNA with larger structural fluctuations tends to have more beneficial mutations.
Article
Genetics & Heredity
Atsushi Shibai, Hazuki Kotani, Natsue Sakata, Chikara Furusawa, Saburo Tsuru
Summary: The expression level of a protein sequence constrains its evolutionary speed, with highly expressed proteins evolving slowly. This study analyzed the genome sequences of 99 strains of E. coli and found that the negative correlation between expression levels and evolutionary rates (E-R anticorrelation) is significant in both past and de novo evolution within the species. The data also confirmed ongoing purifying selection on highly expressed genes, supporting the relevance of underlying mechanisms.
G3-GENES GENOMES GENETICS
(2022)
Article
Microbiology
Shigeyuki Kakizawa, Takahiro Hosokawa, Kohei Oguchi, Kaori Miyakoshi, Takema Fukatsu
Summary: Many insects have facultative symbiotic bacteria, and the prevalence of infection provides important information about the biological impact of these microbial associates. In this study, diverse stinkbugs were surveyed for Spiroplasma infection, revealing a low infection prevalence. Molecular analysis showed that stinkbug-associated Spiroplasma symbionts have multiple evolutionary origins and are not co-speciated with the host stinkbugs. There is a potential for host-symbiont specificity and/or ecological symbiont sharing. Spiroplasma symbionts are generally less abundant than primary gut symbiotic bacteria, localized to various tissues and organs, and vertically transmitted to offspring. They are facultative bacterial associates and not essential for the host stinkbugs, similar to Spiroplasma symbionts of fruit flies and aphids.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Junichiro Iwasawa, Tomoya Maeda, Atsushi Shibai, Hazuki Kotani, Masako Kawada, Chikara Furusawa
Summary: The fitness landscape represents the complex relationship between genotype or phenotype and fitness, allowing for the explanation and prediction of evolutionary trajectories. By inferring the phenotype-based fitness landscape for antibiotic resistance evolution, this study bridges the gap between phenotypic/genotypic changes and fitness, contributing to a better understanding of drug resistance evolution.
Article
Zoology
Soma Chiyoda, Kohei Oguchi, Toru Miura
Summary: This study observed a millipede's molting process and found that during the larval stage, a transparent protrusion containing two pairs of legs appears on each apodous ring, and after molting, two pairs of new legs appear. This suggests that millipedes efficiently grow new legs and rings through the molting process.
FRONTIERS IN ZOOLOGY
(2023)
Article
Microbiology
Taisuke Seike, Hiroki Takekata, Yui Uchida, Natsue Sakata, Chikara Furusawa, Fumio Matsuda
Summary: Two novel yeast species, NBRC 115686T and NBRC 115687, were isolated from flowers and insects in Japan. These strains represent a new species of the genus Wickerhamiella based on sequence analysis and physiological characteristics. The proposed name for this species is Wickerhamiella bidentis sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Evolutionary Biology
Yui Uchida, Hiroyuki Takeda, Chikara Furusawa, Naoki Irie
Summary: Phenotypes with greater developmental stability tend to have stronger evolutionary conservation. Experimental results showed that genes and developmental stages with lower variations led to lower diversity in subsequent generations, suggesting a causal relationship between stability and evolutionary conservation.
Article
Biochemical Research Methods
Yuji Omachi, Nen Saito, Chikara Furusawa
Summary: This study investigates the fitness landscape of the genetic code and finds four major fitness peaks, with one being the standard genetic code. Genetic algorithm analysis suggests that evolution under this multi-peaked fitness landscape is biased towards a narrow peak and is dependent on the evolutionary path.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Ecology
Kenta Kobayashi, Kohei Oguchi, Toru Miura
Summary: In certain termite species, some nymphs can undergo regressive molt where wing buds and body size are reduced. This molt is believed to regulate caste composition in a colony. However, the physiological and developmental processes involved in regressive molt are not well understood. This study observed regressive molt in Hodotermopsis sjostedti termites and examined the histological and morphological changes during this molt. The results showed that nymphs with different types of wing buds underwent different developmental fates, with some differentiating into alates and others becoming workers or other castes. Histological observations revealed degeneration of the epithelial tissue in wing buds during regressive molt, and gene expression analysis showed up-regulation of apoptosis-related factors in the thoracic parts of certain nymphs. Interestingly, the expression pattern of developmental and endocrine factors during regressive molt was similar to that during stationary molt. These findings suggest that the fate of nymph differentiation is determined before molt and that regressive molt is similar to stationary molt.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Kohei Oguchi, Toru Miura
Summary: In termite caste differentiation, Hox genes are upregulated in a caste-specific manner, providing positional identities for body segments and resulting in caste-specific morphogenesis. This study conducted expression and functional analyses of eight Hox genes during soldier, neotenic, and alate differentiation in Hodotermopsis sjostedti, revealing the spatio-temporal patterns of Hox gene expression. RNAi knockdown experiments showed that inhibition of specific Hox genes disrupted caste-specific morphological modifications.
Article
Mathematical & Computational Biology
Masato Tsutsumi, Nen Saito, Daisuke Koyabu, Chikara Furusawa
Summary: This article introduces a deep learning method called Morpho-VAE, which can analyze biological shape features without the need for manual annotations. The method was applied to primate mandible image data and successfully extracted morphological features that reflected the characteristics of different biological families, as well as reconstructed missing segments from incomplete images.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Microbiology
Minoru Moriyama, Yudai Nishide, Atsushi Toyoda, Takehiko Itoh, Takema Fukatsu
Summary: The genomes of obligate bacterial co-symbionts of the green rice leafhopper Nephotettix cincticeps were studied, and it was found that the streamlined genomes of Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola have complementary metabolic pathways for synthesizing essential nutrients required for host adaptation.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biochemistry & Molecular Biology
Yoshinobu Hayashi, Kohei Oguchi, Mayuko Nakamura, Shigeyuki Koshikawa, Toru Miura
Summary: Understanding the processes and consequences of morphological diversity is a major goal in evolutionary biology. This study focused on the annelid family Syllidae, which exhibits remarkable diversity in morphological development. Transcriptome sequencing and genetic analysis of Megasyllis nipponica, a new model species for syllids, identified candidate genes involved in morphogenesis and revealed the occurrence of DNA methylation in its genome. These findings contribute to the molecular understanding of morphogenesis and the morphological diversity in syllids.
GENES & GENETIC SYSTEMS
(2022)
Article
Multidisciplinary Sciences
Sumio Udagawa, Takafumi Ikeda, Kohei Oguchi, Hisanori Kohtsuka, Toru Miura
Summary: This study provides a detailed description of the development process of hydrocoel lobes in the sea cucumber Apostichopus japonicus. The study reveals that cell proliferation is not crucial for lobe formation, while tissue expansion through tissue remodeling contributes to the formation of hydrocoel lobes.
SCIENTIFIC REPORTS
(2022)