Review
Cell Biology
Angela Arabiotorre, Vytas A. Bankaitis, Aby Grabon
Summary: Phosphoinositides are crucial phospholipids in eukaryotes that play important roles in the life processes and signal transduction pathways of apicomplexan parasites. Apicomplexans offer a valuable experimental system for studying the evolution and regulation of phosphoinositide signaling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Sheila C. Nardelli, Natalie C. Silmon de Monerri, Laura Vanagas, Xiaonan Wang, Zoi Tampaki, William J. Sullivan, Sergio O. Angel, Kami Kim
Summary: Histone variants have different distributions in specific regions of the parasite genome, implying their important roles in the developmental transitions of Toxoplasma gondii parasites.
Article
Biotechnology & Applied Microbiology
Eerik Aunin, Matthew Berriman, Adam James Reid
Summary: Genome architecture, reflecting evolutionary pressures, can be characterized using the new tool Genome Decomposition Analysis (GDA). GDA is designed to efficiently explore high-quality genome assemblies and discover hidden features, with demonstrated effectiveness in characterizing genome architectures of single-celled eukaryotic parasites.
Article
Parasitology
Zhenxiao Lu, Hang Hu, Yashan Song, Siyi Zhou, Olalekan Opeyemi Ayanniyi, Qianming Xu, Zhenyu Yue, Congshan Yang
Summary: A prediction model was constructed using machine learning and genomic datasets, and it successfully identified two novel proteins in parasitic protists. Verification showed that these proteins did not affect the growth and replication of the parasite.
PARASITES & VECTORS
(2023)
Article
Chemistry, Medicinal
Renan P. O. Costa, Lucas F. Lucena, Lorena Mara A. Silva, Guilherme Juliao Zocolo, Chonny Herrera-Acevedo, Luciana Scotti, Fernando Batista Da-Costa, Nikita Ionov, Vladimir Poroikov, Eugene N. Muratov, Marcus T. Scotti
Summary: Natural products and their secondary metabolites are crucial for drug discovery, and the SistematX Web Portal provides researchers with important information and tools for studying plant secondary metabolites.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Microbiology
Leonardo Augusto, Jennifer Martynowicz, Parth H. Amin, Kenneth R. Carlson, Ronald C. Wek, William J. Sullivan
Summary: Toxoplasma gondii must balance disseminating throughout its host without killing it, requiring the ability to counter host cell defenses. The parasite mitigates oxidative stress through activation of TgIF2K-B, essential for establishing persistent infection in the host.
Article
Biochemistry & Molecular Biology
Jingjing Lu, Xudong Zhang, Xuan Zhang, Linqi Wang, Ruilin Zhao, Xiao Yong Liu, Xinzhan Liu, Wenying Zhuang, Liang Chen, Lei Cai, Jun Wang
Summary: This study amplifies full-length rRNA operons and establishes a fungal rRNA operon database for improved taxonomic resolution. The study reveals the presence of numerous unknown species in the gut mycobiome and differences in the composition of marine and soil mycobiomes.
Article
Multidisciplinary Sciences
Jose Roberto Rodrigues, Scott W. Roy, Ravinder N. M. Sehgal
Summary: Avian haemosporidian parasites can cause malaria-like symptoms and threaten bird species, and recently, new RNA viruses associated with these parasites have been discovered. Analysis of transcriptome data revealed the presence of two novel RNA viruses associated with different genera of avian haemosporidians.
Article
Biotechnology & Applied Microbiology
Yin Li, Ahmed Mokrani, Huiru Fu, Chenyu Shi, Qi Li, Shikai Liu
Summary: In this study, the researchers developed a full-length transcriptome database of C. gigas using Oxford Nanopore sequencing. They identified thousands of full-length transcripts, alternative splicing events, and alternative polyadenylation sites. Additionally, they conducted integrative analysis of publicly available RNA-seq datasets to understand the transcriptome diversity and post-transcriptional regulation in C. gigas. The researchers also developed a webserver called Cgtdb for transcriptome visualization and functional genome annotation analyses, serving as a valuable resource for the oyster genome annotation.
Article
Biochemistry & Molecular Biology
Luis R. Nassar, Galt P. Barber, Anna Benet-Pages, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Brian T. Lee, Christopher M. Lee, Pranav Muthuraman, Beagan Nguy, Tiana Pereira, Parisa Nejad, Gerardo Perez, Brian J. Raney, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent
Summary: The UCSC Genome Browser, a comprehensive bioinformatics resource, has continued to serve the community for 23 years, with a particular focus on clinical data and SARS-CoV-2. New features and resources, such as the single cell track group and GenArk resource, have been added this year.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Brian T. Lee, Galt P. Barber, Anna Benet-Pages, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Pranav Muthuraman, Luis R. Nassar, Beagan Nguy, Tiana Pereira, Gerardo Perez, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent
Summary: The UCSC Genome Browser is a graphical viewer for exploring genome annotations, providing integrated tools for visualizing, comparing, analyzing, and sharing genomic datasets. Updates this year include new public hub assemblies for new organisms, updated clinical tracks, a new Track Sets feature, enhanced variant displays, and a tool for placing new SARS-CoV-2 genomes in a global phylogenetic tree. Other improvements focus on usability features such as informative mouseover displays and new fonts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Onur Ceylan, Leticia Pereira Ungari, Gonca Soenmez, Cigdem Gul, Ceylan Ceylan, Murat Tosunoglu, Bengi Baycan, Lucia Helena O'Dwyer, Ferda Sevinc
Summary: Although Hepatozoon spp. is the most common intracellular protozoa infecting snakes, its occurrence in snakes from the Colubridae family in Turkiye is limited. This study investigated Hepatozoon spp. in venomous nose-horned vipers from Turkiye. Morphological and molecular methods were used, and positive results for Hepatozoon spp. were found in three snakes. A new species, Hepatozoon viperoi sp. nov., was identified and its genetic relationship with other Hepatozoon species was analyzed. This study expands our knowledge of Hepatozoon species in snakes and contributes to the understanding of haemogregarine protozoan parasites.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Suvarna Nadendla, Rebecca Jackson, James Munro, Federica Quaglia, Balint Meszaros, Dustin Olley, Elizabeth T. Hobbs, Stephen M. Goralski, Marcus Chibucos, Christopher John Mungall, Silvio C. E. Tosatto, Ivan Erill, Michelle G. Giglio
Summary: ECO is a community resource providing an ontology of terms to capture evidence supporting biomedical annotations. Its consistent usage allows for provenance tracking, quality control, and evidence-based data mining. ECO is freely available for download and released under a CC0 1.0 Universal license.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elzbieta Purta, Malgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gulben Avsar, Antonia Romitelli, Pinar Pir, Erik Dassi, Silvestro G. Conticello, Francesca Aguilo, Janusz M. Bujnicki
Summary: MODOMICS database, established since 2006, has evolved from containing basic chemical structures of modified ribonucleosides to a comprehensive resource with new functionalities such as a catalog of RNA modifications linked to human diseases. The database, which is extensively linked to RCSB Protein Data Bank, provides users with an enhanced tool for research on RNA modification.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Microbiology
Ang Hu, Zeming Hu, Haohong Zou, Jiankang Zhang, Dongliang Zhang, Hao Wang, Jianing Zhong, Bin Chen
Summary: This article reviews recent clinical and basic studies on the mechanism and function of CARD9, a crucial mediator in fungal, bacterial, viral, and parasitic infections. The article also summarizes the latest treatment and prevention strategies based on CARD9 and discusses the current perspectives and future directions of CARD9.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Genetics & Heredity
Junya Yamagishi, Kyoko Hayashida, Junji Matsuo, Torahiko Okubo, Makoto Kuroda, Hiroki Nagai, Tsuyoshi Sekizuka, Hiroyuki Yamaguchi, Chihiro Sugimoto
JOURNAL OF HUMAN GENETICS
(2020)
Article
Parasitology
Elisha Chatanga, Henson Kainga, Tinotenda Razemba, Richard Ssuna, Lieza Swennen, Kyoko Hayashida, Chihiro Sugimoto, Ken Katakura, Nariaki Nonaka, Ryo Nakao
Summary: The study revealed that at least 44.5% of dogs in Malawi were infected with tick-borne pathogens, including genera Babesia, Hepatozoon, Anaplasma, and Ehrlichia; education and awareness raising are needed for veterinary practitioners, dog handlers, and pet owners to protect animal health; further research focusing on rural areas is necessary to determine the extent of tick-borne pathogen infection in dogs.
PARASITOLOGY RESEARCH
(2021)
Article
Veterinary Sciences
Yukiko Nakamura, Kyoko Hayashida, Victoire Delesalle, Yongjin Qiu, Ryosuke Omori, Martin Simuunza, Chihiro Sugimoto, Boniface Namangala, Junya Yamagishi
Summary: Using PCR targeting specific sequences, we clarified the genetic diversity of Trypanosoma spp. in the Kafue ecosystem. The findings suggest that T. vivax is the dominant cause of anemia in the area, with extensive diversity among T. vivax-like lineages. Combining CatL PCR with next generation sequencing proves useful in assessing Trypanosoma spp. diversity, especially for T. vivax and T. vivax-like lineages.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Infectious Diseases
Elisha Chatanga, Henson Kainga, Emmanuel Maganga, Kyoko Hayashida, Ken Katakura, Chihiro Sugimoto, Nariaki Nonaka, Ryo Nakao
Summary: Tick-borne diseases caused by Anaplasma, Ehrlichia, Babesia and Theileria are widespread in small ruminants in tropical and sub-tropical countries. The study in Malawi found that 76.6% of sheep and goats tested positive for at least one tick-borne pathogen, with 45% exhibiting co-infections with multiple pathogens. This research represents a significant milestone in understanding and controlling tick-borne pathogens in small ruminants in Malawi.
TICKS AND TICK-BORNE DISEASES
(2021)
Article
Infectious Diseases
Chiho Kaneko, Ryosuke Omori, Michihito Sasaki, Chikako Kataoka-Nakamura, Edgar Simulundu, Walter Muleya, Ladslav Moonga, Joseph Ndebe, Bernard M. Hang'ombe, George Dautu, Yongjin Qiu, Ryo Nakao, Masahiro Kajihara, Akina Mori-Kajihara, Herman M. Chambaro, Hideaki Higashi, Chihiro Sugimoto, Hirofumi Sawa, Aaron S. Mweene, Ayato Takada, Norikazu Isoda
Summary: This study conducted a demographic survey of domestic dogs in rural Zambia and estimated vaccination coverage achievable through mass vaccination campaigns. It found that the majority of the domestic dog population was young, emphasizing the importance of maintaining a 70% annual vaccination coverage in the dog population for rabies control.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Infectious Diseases
Yongjin Qiu, Martin Simuunza, Masahiro Kajihara, Herman Chambaro, Hayato Harima, Yoshiki Eto, Edgar Simulundu, David Squarre, Shiho Torii, Ayato Takada, Bernard Mudenda Hang'ombe, Hirofumi Sawa, Chihiro Sugimoto, Ryo Nakao
Summary: Ticks are important vectors of various pathogens and this study detected Rickettsia and Anaplasmataceae in three different species of argasid ticks collected in Zambia. The study revealed new geographical records of R. lusitaniae and R. hoogstraalii in Africa, highlighting the diversity and distribution of Anaplasma spp.
TICKS AND TICK-BORNE DISEASES
(2021)
Article
Microbiology
Chiho Kaneko, Michihito Sasaki, Ryosuke Omori, Ryo Nakao, Chikako Kataoka-Nakamura, Ladslav Moonga, Joseph Ndebe, Walter Muleya, Edgar Simulundu, Bernard M. Hang'ombe, George Dautu, Masahiro Kajihara, Akina Mori-Kajihara, Yongjin Qiu, Naoto Ito, Herman M. Chambaro, Chihiro Sugimoto, Hideaki Higashi, Ayato Takada, Hirofumi Sawa, Aaron S. Mweene, Norikazu Isoda
Summary: This study investigated the rabies vaccination coverage and antibody levels in owned dog population in Lusaka, Zambia, and assessed the trends of neutralizing antibodies post-vaccination. Findings suggest that a single vaccination with certified vaccines can induce protective antibody levels, while multiple vaccinations resulted in higher antibody titers. The results highlight the importance of continuous booster immunization for maintaining herd immunity and provide valuable information for planning mass rabies vaccination in Zambia.
Article
Parasitology
Elisha Chatanga, Yuma Ohari, Walter Muleya, Kyoko Hayashida, Chihiro Sugimoto, Ken Katakura, Nariaki Nonaka, Ryo Nakao
Summary: This study investigated the population structure of T. parva in Malawi using genetic analysis. The results showed that the isolates in Malawi are closely related to the vaccine component, supporting the use of Muguga cocktail vaccine to control bovine theileriosis.
Article
Parasitology
Elisha Chatanga, Emmanuel Maganga, Wessam Mohamed Ahmed Mohamed, Shohei Ogata, Gita Sadaula Pandey, Abdelbaset Eweda Abdelbaset, Kyoko Hayashida, Chihiro Sugimoto, Ken Katakura, Nariaki Nonaka, Ryo Nakao
Summary: This study conducted a molecular survey on tick-borne pathogens (TBPs) infecting cattle in the central and southern regions of Malawi. The results showed a high burden of TBPs, with 92.3% of the examined animals infected with at least one TBP. Various species of Anaplasmataceae and piroplasms were detected, highlighting the need for new methods to control ticks and TBPs in order to improve animal health and productivity. The newly developed multiplex PCR assay can be a useful tool, especially in resource-limited settings.
Article
Oncology
Shuhei Teranishi, Chihiro Sugimoto, Satoshi Nagaoka, Hirokazu Nagayama, Wataru Segawa, Atsushi Miyasaka, Shuntaro Hiro, Yukihito Kajita, Chihiro Maeda, Nobuaki Kobayashi, Masaki Yamamoto, Makoto Kudo, Takeshi Kaneko
Summary: This retrospective study analyzed the clinical data of 61 patients with EGFR mutation-positive advanced NSCLC who received osimertinib as first-line therapy. The results showed that poor performance status was associated with poor prognosis in these patients.
Article
Oncology
Shuntaro Hiro, Shuhei Teranishi, Tomoe Sawazumi, Satoshi Nagaoka, Chihiro Sugimoto, Hirokazu Nagayama, Wataru Segawa, Yukihito Kajita, Chihiro Maeda, Sousuke Kubo, Kenichi Seki, Ken Tashiro, Nobuaki Kobayashi, Masaki Yamamoto, Makoto Kudo, Takeshi Kaneko
Summary: This study presents a case of a multiple endocrine neoplasia type 1 patient who was diagnosed with atypical carcinoid tumors with elevated mitotic counts. The patient underwent surgery and showed stable disease after treatment. Genetic testing revealed a mutation in the MEN1 gene, confirming the diagnosis of multiple endocrine neoplasia type 1.
Article
Oncology
Chihiro Sugimoto, Shuhei Teranishi, Tomoe Sawazumi, Satoshi Nagaoka, Hirokazu Nagayama, Wataru Segawa, Shuntaro Hiro, Yukihito Kajita, Chihiro Maeda, Sousuke Kubo, Kenichi Seki, Ken Tashiro, Nobuaki Kobayashi, Masaki Yamamoto, Makoto Kudo, Takeshi Kaneko
Summary: Primary tracheal small-cell carcinoma is a rare type of cancer that lacks standard treatment, and is often managed using small-cell lung cancer guidelines. We present a case of a patient who developed nodules in the trachea and left main bronchus following surgery for pulmonary large-cell neuroendocrine carcinoma, which were found to be small-cell carcinoma upon biopsy. The patient experienced respiratory failure due to airway stenosis caused by the growing lesion, but showed improvement after receiving first-line chemotherapy and accelerated hyperfractionated radiotherapy.
Article
Veterinary Sciences
Myagmarsuren Odonchimeg, Dashzevge Erdenechimeg, Adiyasuren Tuvshinbayar, Munkhtuul Tsogtgerel, Enkhbold Bazarragchaa, Ankhanbaatar Ulaankhuu, Tsend Selenge, Dalantai Munkhgerel, Ariunbold Munkhtsetseg, Adilbish Altanchimeg, Raadan Odbileg, Gurdorj Soyolmaa, Yondonjamts Enkhmandakh, Enkhbaatar Batmagnai, Sengee Sugar, Takashi Kimura, Chihiro Sugimoto, Norikazu Isoda, Basan Batsukh, Yoshihiro Sakoda
Summary: This study reports the first outbreak of LSD in Mongolia, with an overall prevalence rate of 5.9% in cattle. Female adults, older cattle, and locations near tube wells and pond water were found to be at higher risk for LSD cases. The newly isolated Mongolian LSD viruses were phylogenetically clustered with Chinese and Vietnamese isolates.
JOURNAL OF VETERINARY MEDICAL SCIENCE
(2022)
Letter
Immunology
Lavel C. Moonga, Kyoko Hayashida, Namwiinga R. Mulunda, Yukiko Nakamura, James Chipeta, Hawela B. Moonga, Boniface Namangala, Chihiro Sugimoto, Zephaniah Mtonga, Mable Mutengo, Junya Yamagishi
Summary: The study found R. asembonensis DNA in human blood samples in Zambia, indicating the possibility of human infection despite its unknown pathogenicity.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Veterinary Sciences
Megasari Marsela, Kyoko Hayashida, Alaa Terkawi, Xuenan Xuan, Chihiro Sugimoto, Junya Yamagishi
JAPANESE JOURNAL OF VETERINARY RESEARCH
(2020)