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Article ; Online: Computational network analysis of host genetic risk variants of severe COVID-19.

Alsaedi, Sakhaa B / Mineta, Katsuhiko / Gao, Xin / Gojobori, Takashi

2023 Volume 17, Issue 1, Page(s) 17

Abstract: Background: Genome-wide association studies have identified numerous human host genetic risk variants that play a substantial role in the host immune response to SARS-CoV-2. Although these genetic risk variants significantly increase the severity of ... ...

Abstract	Background: Genome-wide association studies have identified numerous human host genetic risk variants that play a substantial role in the host immune response to SARS-CoV-2. Although these genetic risk variants significantly increase the severity of COVID-19, their influence on body systems is poorly understood. Therefore, we aim to interpret the biological mechanisms and pathways associated with the genetic risk factors and immune responses in severe COVID-19. We perform a deep analysis of previously identified risk variants and infer the hidden interactions between their molecular networks through disease mapping and the similarity of the molecular functions between constructed networks. Results: We designed a four-stage computational workflow for systematic genetic analysis of the risk variants. We integrated the molecular profiles of the risk factors with associated diseases, then constructed protein-protein interaction networks. We identified 24 protein-protein interaction networks with 939 interactions derived from 109 filtered risk variants in 60 risk genes and 56 proteins. The majority of molecular functions, interactions and pathways are involved in immune responses; several interactions and pathways are related to the metabolic and cardiovascular systems, which could lead to multi-organ complications and dysfunction. Conclusions: This study highlights the importance of analyzing molecular interactions and pathways to understand the heterogeneous susceptibility of the host immune response to SARS-CoV-2. We propose new insights into pathogenicity analysis of infections by including genetic risk information as essential factors to predict future complications during and after infection. This approach may assist more precise clinical decisions and accurate treatment plans to reduce COVID-19 complications.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Genome-Wide Association Study ; Protein Interaction Maps ; Risk Factors
Language	English
Publishing date	2023-03-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2147618-4
ISSN	1479-7364 ; 1479-7364
ISSN (online)	1479-7364
ISSN	1479-7364
DOI	10.1186/s40246-023-00454-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Lactate-mediated neural plasticity genes emerged during the evolution of memory systems.

Bajaffer, Amal / Mineta, Katsuhiko / Magistretti, Pierre / Gojobori, Takashi

Scientific reports

2022 Volume 12, Issue 1, Page(s) 19238

Abstract: The ability to record experiences and learning is present to different degrees in several species; however, the complexity and diversity of memory processes are cognitive function features that differentiate humans from other species. Lactate has ... ...

Abstract	The ability to record experiences and learning is present to different degrees in several species; however, the complexity and diversity of memory processes are cognitive function features that differentiate humans from other species. Lactate has recently been discovered to act as a signaling molecule for neuronal plasticity linked to long-term memory. Because lactate is not only an energy substrate for neurons but also a signaling molecule for plasticity (Magistretti and Allaman in Nat Rev Neurosci 19:235-249, 2018. https://doi.org/10.1038/nrn.2018.19 ), it is of particular interest to understand how and when memory-related genes and lactate-mediated neural plasticity (LMNP) genes emerged and evolved in humans. To understand the evolutionary origin and processes of memory and LMNP genes, we first collected information on genes related to memory and LMNP from the literature and then conducted a comparative analysis of these genes. We found that the memory and LMNP genes have different origins, suggesting that these genes may have become established gradually in evolutionarily and functional terms and not at the same time. We also found that memory and LMNP systems have a similar evolutionary history, having been formed with the gradual participation of newly emerging genes throughout their evolution. We propose that the function of LMNP as a signaling process may be evolutionarily associated with memory systems through an unidentified system that is linked by 13 common genes between memory and LMNP gene sets. This study provides evolutionary insight into the possible relationship between memory and the LMNP systems that deepens our understanding of the evolution of memory systems.
MeSH term(s)	Humans ; Lactic Acid ; Neuronal Plasticity/genetics ; Memory/physiology ; Neurons/physiology ; Signal Transduction
Chemical Substances	Lactic Acid (33X04XA5AT)
Language	English
Publishing date	2022-11-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-23784-8
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Article ; Online: Lactate-mediated neural plasticity genes emerged during the evolution of memory systems

Amal Bajaffer / Katsuhiko Mineta / Pierre Magistretti / Takashi Gojobori

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 9

Abstract: Abstract The ability to record experiences and learning is present to different degrees in several species; however, the complexity and diversity of memory processes are cognitive function features that differentiate humans from other species. Lactate ... ...

Abstract	Abstract The ability to record experiences and learning is present to different degrees in several species; however, the complexity and diversity of memory processes are cognitive function features that differentiate humans from other species. Lactate has recently been discovered to act as a signaling molecule for neuronal plasticity linked to long-term memory. Because lactate is not only an energy substrate for neurons but also a signaling molecule for plasticity (Magistretti and Allaman in Nat Rev Neurosci 19:235–249, 2018. https://doi.org/10.1038/nrn.2018.19 ), it is of particular interest to understand how and when memory-related genes and lactate-mediated neural plasticity (LMNP) genes emerged and evolved in humans. To understand the evolutionary origin and processes of memory and LMNP genes, we first collected information on genes related to memory and LMNP from the literature and then conducted a comparative analysis of these genes. We found that the memory and LMNP genes have different origins, suggesting that these genes may have become established gradually in evolutionarily and functional terms and not at the same time. We also found that memory and LMNP systems have a similar evolutionary history, having been formed with the gradual participation of newly emerging genes throughout their evolution. We propose that the function of LMNP as a signaling process may be evolutionarily associated with memory systems through an unidentified system that is linked by 13 common genes between memory and LMNP gene sets. This study provides evolutionary insight into the possible relationship between memory and the LMNP systems that deepens our understanding of the evolution of memory systems.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Current trends in RNA virus detection through metatranscriptome sequencing data.

Nakagawa, So / Sakaguchi, Shoichi / Ogura, Atsushi / Mineta, Katsuhiko / Endo, Toshinori / Suzuki, Yoshiyuki / Gojobori, Takashi

FEBS open bio

2023 Volume 13, Issue 6, Page(s) 992–1000

Abstract: With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled ...

Abstract	With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/genetics ; RNA Viruses/genetics ; RNA, Viral/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-05-20
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13626
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Article ; Online: Significant variants of type 2 diabetes in the Arabian Region through an Integration of exome databases.

Goto, Kosuke / Mineta, Katsuhiko / Miyazaki, Satoru / Gojobori, Takashi

PloS one

2021 Volume 16, Issue 4, Page(s) e0249226

Abstract: Type 2 diabetes (T2D) is a major global health issue, and it has also become one of the major diseases in Arab countries. In addition to the exome databases that have already been established, whole exome sequencing data for the Greater Middle East are ... ...

Abstract	Type 2 diabetes (T2D) is a major global health issue, and it has also become one of the major diseases in Arab countries. In addition to the exome databases that have already been established, whole exome sequencing data for the Greater Middle East are now available. To elucidate the genetic features of T2D in the Arabian Peninsula, we integrated two exome databases (gnomAD exome and the Greater Middle East Variome Project) with clinical information from the ClinVar. After the integration, we obtained 18 single nucleotide polymorphisms and found two statistically and clinically significant variants in two genes, SLC30A8 rs13266634 and KCNJ11 rs5219. Interestingly, the two genes are linked to the uptake of the metals, Zn and K respectively, which indicating the regional features of the genetic variants. The frequency of the risk allele of rs13266634 among individuals in the Arabian Peninsula was higher than among individuals in other regions. On the other hand, the frequency of the risk allele of rs5219 in the Arabian Peninsula was lower than that in other regions. We identified and characterized T2D-related variants that show unique tendencies in the Arabian Peninsula. Our analyses contribute to and provide guidance for the clinical research of T2D in the Arabian Peninsula.
Language	English
Publishing date	2021-04-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0249226
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Article ; Online: Evolution of memory system-related genes.

Bajaffer, Amal / Mineta, Katsuhiko / Gojobori, Takashi

FEBS open bio

2021 Volume 11, Issue 12, Page(s) 3201–3210

Abstract: Memory has an essential function in human life as it helps individuals remember and recognize their surroundings. It is also the major form of cognition that controls behavior. As memory is a function that is highly characteristic of humans, how it was ... ...

Abstract	Memory has an essential function in human life as it helps individuals remember and recognize their surroundings. It is also the major form of cognition that controls behavior. As memory is a function that is highly characteristic of humans, how it was established is of particular interest. Recent progress in the field of neurosciences, together with the technological advancement of genome-wide approaches, has led to the accumulation of evidence regarding the presence and similar/distinct mechanisms of memory among species. However, the understanding of the evolution of memory obtained utilizing these genome-wide approaches remains unclear. The purpose of this review was to provide an overview of the literature on the evolution of the memory system among species and the genes involved in this process. This review also discusses possible approaches to study the evolution of memory systems to guide future research.
MeSH term(s)	Animals ; Biological Evolution ; Cognition/physiology ; Genome, Human/genetics ; Humans ; Memory/physiology
Language	English
Publishing date	2021-06-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13224
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Article ; Online: A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution.

Noro, Yukihiko / Shimizu, Hiroshi / Mineta, Katsuhiko / Gojobori, Takashi

Scientific reports

2021 Volume 11, Issue 1, Page(s) 10828

Abstract: The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria are well ... ...

Abstract	The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria are well conserved in Cnidaria. Thus, the cnidarian Hydra vulgaris is a good model organism for the study of the putative primitive nervous system in its last common ancestor. The diffuse nervous system of Hydra consists of several peptidergic neuron subsets. However, the specific functions of these subsets remain unclear. Using calcium imaging, here we show that the neuron subsets that express neuropeptide, Hym-176, function as motor circuits to evoke longitudinal contraction. We found that all neurons in a subset defined by the Hym-176 gene (Hym-176A) or its paralogs (Hym-176B) expression are excited simultaneously, followed by longitudinal contraction. This indicates not only that these neuron subsets have a motor function but also that a single molecularly defined neuron subset forms a single coactive circuit. This is in contrast with the bilaterian nervous system, where a single molecularly defined neuron subset harbors multiple coactive circuits, showing a mixture of neurons firing with different timings. Furthermore, we found that the two motor circuits, one expressing Hym-176B in the body column and the other expressing Hym-176A in the foot, are coordinately regulated to exert region-specific contraction. Our results demonstrate that one neuron subset is likely to form a monofunctional circuit as a minimum functional unit to build a more complex behavior in Hydra. This simple feature (one subset, one circuit, one function) found in Hydra may represent the simple ancestral condition of neural evolution.
MeSH term(s)	Animals ; Biological Evolution ; Calcium Signaling ; Hydra/metabolism ; Hydra/physiology ; Molecular Imaging/veterinary ; Neurons/physiology ; Neuropeptides/metabolism ; Tissue Distribution
Chemical Substances	Hym-176 protein, Hydra ; Neuropeptides
Language	English
Publishing date	2021-05-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-89325-x
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Article ; Online: Current trends in RNA virus detection through metatranscriptome sequencing data

So Nakagawa / Shoichi Sakaguchi / Atsushi Ogura / Katsuhiko Mineta / Toshinori Endo / Yoshiyuki Suzuki / Takashi Gojobori

FEBS Open Bio, Vol 13, Iss 6, Pp 992-

2023 Volume 1000

Abstract	With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.
Keywords	endogenous viral elements ; metatranscriptome ; RNA virome ; RNA‐dependent RNA polymerase ; SARS‐CoV‐2 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evolution of memory system‐related genes

Amal Bajaffer / Katsuhiko Mineta / Takashi Gojobori

FEBS Open Bio, Vol 11, Iss 12, Pp 3201-

2021 Volume 3210

Abstract	Memory has an essential function in human life as it helps individuals remember and recognize their surroundings. It is also the major form of cognition that controls behavior. As memory is a function that is highly characteristic of humans, how it was established is of particular interest. Recent progress in the field of neurosciences, together with the technological advancement of genome‐wide approaches, has led to the accumulation of evidence regarding the presence and similar/distinct mechanisms of memory among species. However, the understanding of the evolution of memory obtained utilizing these genome‐wide approaches remains unclear. The purpose of this review was to provide an overview of the literature on the evolution of the memory system among species and the genes involved in this process. This review also discusses possible approaches to study the evolution of memory systems to guide future research.
Keywords	evolution ; memory ; episodic memory ; long‐term potentiation ; sensitization ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Inter-library loan at ZB MED

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Article ; Online: A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution

Yukihiko Noro / Hiroshi Shimizu / Katsuhiko Mineta / Takashi Gojobori

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 12

Abstract: Abstract The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria ... ...

Abstract	Abstract The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria are well conserved in Cnidaria. Thus, the cnidarian Hydra vulgaris is a good model organism for the study of the putative primitive nervous system in its last common ancestor. The diffuse nervous system of Hydra consists of several peptidergic neuron subsets. However, the specific functions of these subsets remain unclear. Using calcium imaging, here we show that the neuron subsets that express neuropeptide, Hym-176, function as motor circuits to evoke longitudinal contraction. We found that all neurons in a subset defined by the Hym-176 gene (Hym-176A) or its paralogs (Hym-176B) expression are excited simultaneously, followed by longitudinal contraction. This indicates not only that these neuron subsets have a motor function but also that a single molecularly defined neuron subset forms a single coactive circuit. This is in contrast with the bilaterian nervous system, where a single molecularly defined neuron subset harbors multiple coactive circuits, showing a mixture of neurons firing with different timings. Furthermore, we found that the two motor circuits, one expressing Hym-176B in the body column and the other expressing Hym-176A in the foot, are coordinately regulated to exert region-specific contraction. Our results demonstrate that one neuron subset is likely to form a monofunctional circuit as a minimum functional unit to build a more complex behavior in Hydra. This simple feature (one subset, one circuit, one function) found in Hydra may represent the simple ancestral condition of neural evolution.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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