Special & Virtual Issues from The Journal of Biochemistry

For information on forthcoming Special and Virtual Issues and details of how to contribute, please click here.

2025

Special Issue: Biochemistry of Aging: Latest Insights into Aging and Cellular Senescence (March 2025)

Guest Editor:  

Akiko Takahashi

Analysis of the mechanisms that control the lifespan of organisms has expanded greatly from research using model organisms such as yeasts, nematodes and fishes to research using mammals such as mice and marmosets. In particular, advances in cellular senescence research are progressing in the analysis of the previously unknown basic mechanisms of individual aging and the onset mechanisms of age-related diseases. Senolytics, which controls senescent cells in humans, is attracting worldwide attention. This symposium aims to deepen our understanding of the biochemistry of aging by sharing and discussing the latest findings in aging and cellular senescence research.

2024

Special Issue: Physiological and pathological organ remodeling and plasticity (October 2024)

Guest Editor:

Fumiko Toyoshima

Each organ within a living body reorganizes in response to physiological changes associated with different life stages and lifestyles. It is becoming clear that this physiological organ remodeling is a mechanism that involves tissue regeneration and plasticity and is essential for maintaining homeostasis in the living body. In contrast, organ remodeling associated with disease and aging induces chronic inflammation and fibrosis and decreases tissue plasticity. This special issue, Physiological and Pathological Organ Remodeling and Plasticity, will introduce the physiological and pathological organ remodeling mechanisms of various organs and applications in regenerative medicine and anti-aging.

Special Issue: New frontiers in ubiquitin research (May 2024)

Guest Editors:

Yasushi Saeki and Shigeo Murata

The functional diversity of ubiquitin is attributed to the structural diversity of ubiquitin modifications called the 'ubiquitin code'. Because these ubiquitin codes are more diverse and dynamic than expected, and the decoder molecules are also diverse, the ubiquitin codes remain comprehensively elucidated. In many cases, ubiquitination induces proteasome-mediated degradation, but the molecular mechanism remains largely unknown. Although the number of ubiquitin-related diseases is increasing, a limited number of pathogenic mechanisms have been elucidated. Under these circumstances, there is an urgent need for research methods and tools to analyze each ubiquitin-dependent pathway. This special issue, "New frontiers in ubiquitin research" will focus on novel insights into ubiquitin biology and diseases, drug discovery, and emerging technologies.

Special Issue: Multi-scale platform for GPCR biology (April 2024)

Guest Editors:

Asuka inoue, Arun K. Shukla

To build a technological platform that enables the digital reconstruction of physiological processes, components of complex physiological processes and information processing mechanisms in the body should be quantitatively elucidated. Moreover, the elementary processes at each scale from molecules to cells and should be analyzed. In this special issue, the Multi-scale platform for GPCR biology will focus on recent progress to combine highly original analytical techniques at each scale to understand the function of GPCR.

Dynamic zoning of cytoplasm by membranes and phase separation (February 2024)

Guest Editors:

Nobuo Noda, Masaaki Komatsu

The cytoplasm is complexly compartmentalized (zoned) by lipid membranes and phase separation, allowing various signal transmissions and enzymatic reactions to proceed smoothly, without interference. Autophagy research on various pathways has revealed that it has a significant impact on cytoplasmic zoning. Autophagy not only creates a new cytoplasmic zone through autophagosome formation but further contributes to cytoplasmic zoning through organelle deformation, reorganization of membrane organelles such as the endoplasmic reticulum and mitochondria, and selective disassembly of phase-separated droplets. This special issue, Dynamic zoning of cytoplasm by membranes and phase separation, views autophagy as a reorganization mechanism of cytoplasmic zoning, discusses its various mechanisms, and introduces the world of cytoplasmic zoning including topics other than autophagy.

2023

Multifaceted Protein World (April 2023)

Guest Editors:

Hideki Taguchi and Richard I. Morimoto

Ribosome is a hub for protein functions and is crucial for the folding, targeting, and quality control of proteins. The field has been significantly advanced by the development of experimental tools that enable to determine the ribosome occupancy in a nucleotide-level resolution and quantitative proteomics by bottom-up proteomics. This special issue, Multifaceted Protein World will focus on novel biological features and regulations of protein synthesis, and protein dynamics including proofreading of protein localization and liquid–liquid phase separation.

Stromal Cell Biology (March 2023)

Guest Editors:

Masanori Aikawa, Yumiko Oishi and Ichiro Manabe

The stroma is not merely the supporting tissue of an organ, but also the site where diverse cells dynamically interact to maintain organ homeostasis. The stroma is also the primary site of inflammatory processes. In this issue, four review articles summarize recent advances in the function and regulation of immune cells in the stroma in physiology and pathology.

2022

The Journal of Biochemistry 100th Anniversary Issue (September 2022)

The Journal of Biochemistry (JB) has just celebrated its 100th anniversary and I would like to express my sincere gratitude to the efforts of the successive Editors-in-Chief who have made it possible for JB to develop as a leading scientific journal in biochemistry and life sciences over such a long period of time. This special issue marks the 100th anniversary of the journal and we would like to thank Dr Mark A. Lemmon, Chair of the Editorial Board of the Biochemical Journal, and Dr Seamus J. Martin, Editor-in-Chief of the FEBS Journal, for their kind words of congratulations. Both journals, like JB, share a mission to serve the scientific community and are responding to major changes in the current scientific journal publishing industry, including the rise of open access and commercial journals, with a common awareness of the issues involved. The role of academic journals is not only to disseminate scientific results to the world, but also to contribute to the development of professional societies, the training of young researchers and the promotion of international exchange. Indeed, I am very proud to have published my first paper, which was also my dissertation, in JB. When I was a graduate student, I presented the results of my research every year at the annual meeting of the Japanese Biochemical Society and received comments from various professors, sometimes harsh, sometimes encouraging, as I advanced my own research. The journal must keep pace with such society activities and contribute to the scientific community.

Ever-expanding NGLY1 biology (February 2022)

Guest Editors:

Tadashi Suzuki and Yukiko Yoshida

The cytosolic peptide: N-glycanase (PNGase; NGLY1 in humans) is a deglycosylating enzyme that is widely conserved in eukaryotes. This enzyme is involved in the degradation of misfolded N-glycoproteins that are destined for proteasomal degradation in the cytosol, a process that is called endoplasmic reticulum-associated degradation. Although the physiological significance of NGLY1 remained unknown until recently, the discovery of NGLY1 deficiency, a human genetic disorder bearing mutations in the NGLY1 gene, has led to explosive research progress regarding the functional characterization of this enzyme. For example, it is now known that NGLY1 can also act as an ‘editing enzyme’ to convert N-glycosylated asparagine residues to aspartate residues, thus introducing negative charges into a core peptide and modulating the function of the target molecule. Diverse biological processes have also been found to be affected by compromised NGLY1 activity. In this special issue, recent research progress on the functional characterization of NGLY1 and its orthologues in worm/fly/rodents, assay methods/biomarkers useful for the development of therapeutics and the comprehensive transcriptome/proteome of NGLY1-KO cells as well as patient-derived cells are discussed.

Protein Data Bank 50th Anniversary Virtual Issue: Featured articles from The Journal of Biochemistry

Guest Editor:

Genji Kurisu

Protein Data Bank (PDB) was born on October 20th, 1971 with only 7 crystallographic entries, but now grown as the single global archive holding more than 180,000 entries of experimentally determined biological macromolecular structures by X-ray crystallography, NMR spectroscopy and 3D cryogenic electron microscopy. From the beginning of PDB, the Journal of Biochemistry keeps being one of major publication platforms for the structural reports especially in Asia, which means JB has been with PDB for half of its publishing history of 100 years. Structural biologists joined the editorial board of JB as a section editor or associated editor for a long time, encouraging authors to deposit their structures to JB. This long history between JB and PDB has resulted in high citation numbers for structural reports in it. In this virtual issue, we celebrate the 50th anniversary of PDB by highlighting the top 10 articles of higher citation numbers and top 5 articles with highest resolution published in JB since 1971, together with two papers of 1st NMR structure and one database article in JB.

PDB 50th Anniversary Issue - 50 years of Protein Data Bank in JB (January 2022)

Guest Editor:

Genji Kurisu

Protein Data Bank (PDB), jointly founded in 1971 by Brookhaven National Laboratory, U.S.A. and the Cambridge Crystallographic Data Centre, U.K, is the single global archive of experimentally determined biological macromolecular structures. PDB deposition is mandatory for structural publication in most scientific journals, which means “no PDB deposition, no structural publication”. The current PDB archive contains more than 180,000 entries and includes many structures from Asian institutions. The first protein structure in PDB from Asia was that of Cytochrome c determined by Prof. Masao Kakudo’s group at the Institute for Protein Research, Osaka University, at a resolution of originally 4 Å, and subsequently 2.3 Å resolution as the 21st entry of the entire PDB archive, both of which were published in the Journal of Biochemistry as the structural report. Since then, 317 protein structures whose primary citation was JB have been deposited to PDB. Based on this long history between PDB and JB, the yearly distribution, resolution, quality of structure, type of target protein, number of citations and comparison against other major journals of all structural reports in JB were reviewed statistically using the relational database system at PDBj (https://pdbj.org). Additionally, five highly sited reports in JB were selected and the original author(s) or succeeding research group, including one of original authors at least, reviewed the research background when originally published and the current status of research research-field further developed later.   

2021

Nucleoskeleton-oriented nuclear architecture and dynamics to regulate genome functions (March 2021)

Guest Editors:

Masahiko Harata, Kei Miyamoto and Piergiorgio Percipalle

In eukaryotes, nuclear architecture and dynamics affect chromatin structure, and regulate biological functions such as embryonic development, cellular differentiation, aging and/or diseases. Nucleoskeleton proteins such as nuclear actin and lamin have attracted much attention as regulators of nuclear architecture and dynamics, and it has been recently demonstrated that these nucleoskeleton proteins play important roles in genomic functions such as transcription and DNA repair. The field has been significantly advanced by the development of experimental tools that enable spatiotemporal control and monitoring of nuclear dynamics. This special issue will focus on novel biological features of nucleoskeleton proteins and the state-of-the-art technologies for regulating nuclear architecture and dynamics.

Medical chemistry of extracellular vesicles (February 2021)

Guest Editors:

Rikinari Hanayama and Juan S. Bonifacino

Extracellular vesicles (EVs) such as exosomes and microvesicles serve as messengers of intercellular communication networks, allowing the exchange of proteins and lipids between their producing cells and target cells that trigger various cellular responses. EVs also carry mRNAs and microRNAs inside them, raising the possibility that EVs transfer genetic information among cells. However, the physiological and pathophysiological functions of EVs remain largely elusive. In this issue, we summarize the latest outstanding findings that unveiled novel functions of EVs.

2020

Dynamics Regulation of Mitochondria (March 2020)

Guest Editors:

Naotada Ishihara and Howard Jacobs

Mitochondria are double-membrane organelles containing their own DNA (mtDNA). Mitochondria play an important role, not only in energy production through oxidative phosphorylation, but they also have regulatory functions such as cell death, signaling, development, and metabolism. Mitochondria are dynamic organelle, changing their morphology by active membrane fusion and fission in response to various cellular signaling. This special issue will focus on the dynamic features of pleiotropic mitochondria, under cellular signaling and differentiation in vivo.

Redox Metabolism and Signaling (February 2020)

Guest Editors:

Motohiro Nishida and Albert van der Vliet

A new concept of life sciences has been revealed by sulfur-based redox biology. Living systems use redox potential-based energy metabolism and stress response to maintain living homeostasis.  Redox research has been developed by investigating pathophysiological roles of specific signaling pathways induced by chemical modification of intracellular molecules with oxygen-derived byproducts of energy metabolism, including reactive oxygen species (ROS) and electrophiles. Recently, reactive sulfide species, represented by persulfide and polysulfide, have been revealed to function as endogenous nucleophile that can react with, metabolize, and eliminate electrophiles.  These reactive sulfides are also found to participate in physiological energy metabolism coupling with electron transfer and formation of iron-sulfur clusters. This issue summarizes cutting-edge research on the molecular bases of sulfur-based redox signaling and their new biological roles in living systems.