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JOURNAL ARTICLE
Toshihiro Tokiwa, Momo Fushimi, Shyun Chou, Akemi Yoshida, Kensei Kinoshita, Atsushi Hikima, Taisei Kikuchi, Kiyokazu Ozaki
BACKGROUND: Sparganosis is a rare zoonotic disease caused by plerocercoid larvae of the genera Spirometra or Sparganum (Cestoda: Diphyllobothriidae). The larvae of Spirometra generally do not undergo asexual reproduction, whereas those of Sparganum can induce proliferative lesions in infected tissues. This paper presents an unusual case of proliferative sparganosis due to infection with Spirometra mansoni in a cat, normally considered a definitive host of the species. CASE PRESENTATION: A 9-year-old male domestic cat was presented with a mass on the right side of the face that underwent progressive enlargement for 1 month...
April 20, 2024: BMC Veterinary Research
#22
JOURNAL ARTICLE
Tamara Teodoro Araujo, Aline Dionizio, Thamyris Souza Carvalho, Chelsea Maria Vilas Boas Feitosa, Mariele Vertuan, João Victor Frazão Câmara, Flavio Henrique-Silva, Reinaldo Marchetto, Marcos Roberto Chiaratti, Angélica Camargo Santos, Lindomar Oliveira Alves, Milene Ferro, Marília Afonso Rabelo Buzalaf
OBJECTIVE: This study was designed in two-legs. In the in vivo, we explored the potential of a rinse solution containing a combination (Comb) of 0.1 mg/mL CaneCPI-5 (sugarcane-derive cystatin), 1.88 × 10- 5 M StN15 (statherin-derived peptide) and 1.0 mg/mL hemoglobin (Hb) to change the protein profile of the acquired enamel pellicle(AEP) and the microbiome of the enamel biofilm. The in vitro, was designed to reveal the effects of Comb on the viability and bacterial composition of the microcosm biofilm, as well as on enamel demineralization...
April 20, 2024: Clinical Oral Investigations
#23
JOURNAL ARTICLE
Job P van Kooten, Michelle V Dietz, Hendrikus Jan Dubbink, Cornelis Verhoef, Joachim G J V Aerts, Eva V E Madsen, Jan H von der Thüsen
Peritoneal mesothelioma (PeM) is an aggressive tumor with limited treatment options. The current study aimed to evaluate the value of next generation sequencing (NGS) of PeM samples in current practice. Foundation Medicine F1CDx NGS was performed on 20 tumor samples. This platform assesses 360 commonly somatically mutated genes in solid tumors and provides a genomic signature. Based on the detected mutations, potentially effective targeted therapies were identified. NGS was successful in 19 cases. Tumor mutational burden (TMB) was low in 10 cases, and 11 cases were microsatellite stable...
April 20, 2024: Clinical and Experimental Medicine
#24
REVIEW
Noriko Miyake
Diseases are caused by genetic and/or environmental factors. It is important to understand the pathomechanism of monogenic diseases that are caused only by genetic factors, especially prenatal- or childhood-onset diseases for pediatricians. Identifying "novel" disease genes and elucidating how genomic changes lead to human phenotypes would develop new therapeutic approaches for rare diseases for which no fundamental cure has yet been established. Genomic analysis has evolved along with the development of analytical techniques, from Sanger sequencing (first-generation sequencing) to techniques such as comparative genomic hybridization, massive parallel short-read sequencing (using a next-generation sequencer or second-generation sequencer) and long-read sequencing (using a next-next generation sequencer or third-generation sequencer)...
2024: Pediatrics International: Official Journal of the Japan Pediatric Society
#25
REVIEW
David-Alexandre Trégouët, Morange Pierre-Emmanuel
This invited review follows the oral presentation "To Sequence or Not to Sequence, That Is Not the Question; But "When, Who, Which and What For?" Is " given during the State Of the Art session Translational Genomics in Thrombosis: From OMICs to Clinics" of the ISTH 2023 congress. Emphasizing the power of next-generation sequencing technologies and the diverse strategies associated with DNA variant analysis, this review highlights the unresolved questions and challenges in their implementation both for the clinical diagnosis of venous thromboembolism and in translational research...
April 17, 2024: Journal of Thrombosis and Haemostasis: JTH
#26
JOURNAL ARTICLE
Chunping Sun, Chaoe Zhou, Lina Wang, Shanchen Wei, Mingwei Shi, Jun Li, Lianjun Lin, Xinmin Liu
Metagenomic next-generation sequencing (mNGS) has become an available method for pathogen detection. The clinical application of mNGS requires further evaluation. We conducted a cross-sectional study of 104 patients with suspected infection between May 2019 and May 2021. The risk factors associated with infection were analyzed using univariate logistic analysis. The diagnostic performance of pathogens was compared between mNGS and conventional microbiological tests. About 104 patients were assigned into 3 groups: infected group (n = 69), noninfected group (n = 20), and unknown group (n = 15)...
April 19, 2024: Medicine (Baltimore)
#27
JOURNAL ARTICLE
Shouxia Li, Shurui Li, Dingli Chen, Subin Zhao, Cairu Liu, Ruimin Zhang, Yongxue Chen, Xiangrui Guo, Xuedong Song
RATIONALE: Hereditary hearing loss is known to exhibit a significant degree of genetic heterogeneity. Herein, we present a case report of a novel mutation in the tenascin-C (TNC) gene in Chinese patients with nonsyndromic hearing loss (NSHL). PATIENT CONCERNS: This includes a young deaf couple and their 2-year-old baby. DIAGNOSES: Based on the clinical information, hearing test, metagenomic next-generation sequencing (mNGS), Sanger sequencing, protein function and structure analysis, and model prediction, in our case, the study results revealed 2 heterozygous mutations in the TNC gene (c...
April 19, 2024: Medicine (Baltimore)
#28
JOURNAL ARTICLE
Dimyana Neufeldt, Arne Schmidt, Elisa Mohr, Dongchao Lu, Shambhabi Chatterjee, Maximilian Fuchs, Ke Xiao, Wen Pan, Sarah Cushman, Christopher Jahn, Malte Juchem, Hannah Jill Hunkler, Giuseppe Cipriano, Bjarne Jürgens, Kevin Schmidt, Sonja Groß, Mira Jung, Jeannine Hoepfner, Natalie Weber, Roger Foo, Andreas Pich, Robert Zweigerdt, Theresia Kraft, Thomas Thum, Christian Bär
Hypertrophic cardiomyopathy (HCM) constitutes the most common genetic cardiac disorder. However, current pharmacotherapeutics are mainly symptomatic and only partially address underlying molecular mechanisms. Circular RNAs (circRNAs) are a recently discovered class of non-coding RNAs and emerged as specific and powerful regulators of cellular functions. By performing global circRNA-specific next generation sequencing in cardiac tissue of patients with hypertrophic cardiomyopathy compared to healthy donors, we identified circZFPM2 (hsa_circ_0003380)...
April 19, 2024: Basic Research in Cardiology
#29
JOURNAL ARTICLE
Simone Filardo, Marisa Di Pietro, Rosa Sessa
It is becoming increasingly clear that the human microbiota, also known as "the hidden organ", possesses a pivotal role in numerous processes involved in maintaining the physiological functions of the host, such as nutrient extraction, biosynthesis of bioactive molecules, interplay with the immune, endocrine, and nervous systems, as well as resistance to the colonization of potential invading pathogens. In the last decade, the development of metagenomic approaches based on the sequencing of the bacterial 16s rRNA gene via Next Generation Sequencing, followed by whole genome sequencing via third generation sequencing technologies, has been one of the great advances in molecular biology, allowing a better profiling of the human microbiota composition and, hence, a deeper understanding of the importance of microbiota in the etiopathogenesis of different pathologies...
2024: Frontiers in Cellular and Infection Microbiology
#30
JOURNAL ARTICLE
Mao Suganami, Soichi Kojima, Hideki Yoshida, Masaki Mori, Mayuko Kawamura, Eriko Koketsu, Makoto Matsuoka
In the early 1900s, mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of next-generation sequencing (NGS) technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using NGS to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism...
2024: Frontiers in Plant Science
#31
JOURNAL ARTICLE
Xiaofen Li, Nan Zhou, Yu Yang, Zijian Lu, Hongfeng Gou
Biliary tract cancer (BTC) is a highly aggressive malignancy with limited second-line therapy. We conducted this phase 2 trial to evaluate the efficacy and safety of second-line nab-paclitaxel plus sintilimab in advanced BTC. Histologically confirmed advanced BTC patients with documented disease progression after first-line chemotherapy were enrolled. Subjects received nab-paclitaxel 125 mg/m2 on days 1 and 8 plus sintilimab 200 mg on day 1, administered every 3 weeks. The primary end point was the objective response rate (ORR)...
April 18, 2024: Cancer Science
#32
JOURNAL ARTICLE
Jianqiao Hu, Sai Luo, Ming Tian, Adam Yongxin Ye
BACKGROUND: High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, 'N's. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address 'N's correctly or efficiently...
April 18, 2024: BMC Bioinformatics
#33
Erika Uehara, Naoaki Hori, Kanako Tanase-Nakao, Kazuhisa Akiba, Hidefumi Sueoka, Keiko Matsubara, Satoshi Narumi
INTRODUCTION: NK2 homeobox 1 (NKX2-1) encodes a transcription factor NKX2-1 that is expressed in the thyroid gland, lung and brain. Dual oxidase 2 (DUOX2) encodes an enzyme which generates hydrogen peroxide and is involved in the thyroid hormone synthesis. Cases of congenital hypothyroidism (CH) with dyshormonogenesis showing two or more genetic variants are increasingly reported. We describe the first case of transient dyshormonogenesis who had experimentally-verified a loss of function NKX2-1 variant and DUOX2 variants...
April 18, 2024: Hormone Research in Pædiatrics
#34
JOURNAL ARTICLE
Hao Chen, Zubing Xu, Yu Zhou, Yu-Huan Jiang, Jin Chen, Yingqiong Xiong, Meihong Zhou, Xiaomu Wu, Daojun Hong
BACKGROUND: Recent evidence shows that immunosuppressive agents can affect the gut microbiota in autoimmune diseases. However, the relationship between the gut microbiome and B-cell depletion immunotherapy in neuromyelitis optica spectrum disorder (NMOSD) remains poorly understood. OBJECTIVES: To evaluate the distinct intestinal microbial patterns and serum cytokine levels after short-term rituximab treatment (three months) in patients with NMOSD. METHODS: Firstly, we conducted a cross-sectional study involving 46 treatment-naïve NMOSD patients and 48 matched healthy controls...
April 16, 2024: Multiple Sclerosis and related Disorders
#35
JOURNAL ARTICLE
Joaquin Garcia-Solorio, Juan Carlos Núñez-Enriquez, Marco Jiménez-Olivares, Janet Flores-Lujano, Fernanda Flores-Espino, Carolina Molina-Garay, Alejandra Cervera, Diana Casique-Aguirre, José Gabriel Peñaloza-Gonzalez, Ma Del Rocío Baños-Lara, Ángel García-Soto, César Alejandro Galván-Díaz, Alberto Olaya-Vargas, Hilario Flores Aguilar, Minerva Mata-Rocha, Miguel Ángel Garrido-Hernández, Juan Carlos Solís-Poblano, Nuria Citlalli Luna-Silva, Lena Sarahi Cano-Cuapio, Pierre Mitchel Aristil-Chery, Fernando Herrera-Quezada, Karol Carrillo-Sanchez, Anallely Muñoz-Rivas, Luis Leonardo Flores-Lagunes, Elvia Cristina Mendoza-Caamal, Beatriz Eugenia Villegas-Torres, Vincent González-Osnaya, Elva Jiménez-Hernández, José Refugio Torres-Nava, Jorge Alfonso Martín-Trejo, María de Lourdes Gutiérrez-Rivera, Rosa Martha Espinosa-Elizondo, Laura Elizabeth Merino-Pasaye, María Luisa Pérez-Saldívar, Silvia Jiménez-Morales, Everardo Curiel-Quesada, Haydeé Rosas-Vargas, Juan Manuel Mejía-Arangure, Carmen Alaez-Verson
BACKGROUND: Recurrent genetic alterations contributing to leukemogenesis have been identified in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL), and some are useful for refining classification, prognosis, and treatment selection. IKZF1plus is a complex biomarker associated with a poor prognosis. It is characterized by IKZF1 deletion coexisting with PAX5 , CDKN2A/2B , or PAR1 region deletions. The mutational spectrum and clinical impact of these alterations have scarcely been explored in Mexican pediatric patients with B-ALL...
2024: Frontiers in Oncology
#36
JOURNAL ARTICLE
Yong Gao, Si Yin
The mountainous region of southern China has been characterized by its complicated environment and topography. Amorphophallus kiusianus Makino 1913 is a representative species of extreme habitat preference that resides mainly in this region. To help study the genetic differentiation mechanisms of A. kiusianus populations, we sequenced the first chloroplast genome of this species using next-generation sequencing. The chloroplast genome was 166,269 bp in length with an average GC content of 36% (GenBank accession number: PP072243)...
2024: Mitochondrial DNA. Part B. Resources
#37
JOURNAL ARTICLE
Adrián César-Razquin, Josep Casacuberta, Tamas Dalmay, Silvia Federici, Sara Jacchia, Dafni Maria Kagkli, Simon Moxon, Nikoletta Papadopoulou
As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants...
April 2024: EFSA journal
#38
JOURNAL ARTICLE
Liyan Zhang, Xueqing Liu, Bijun Fan, Jiajun Chen, Jie Chen, Qiuhong Li, Xueling Wu
BACKGROUND: Interstitial lung disease (ILD) is a common complication of idiopathic inflammatory myopathy (IIM), which is one of the connective tissue diseases (CTD). It can lead to poor prognosis and increased mortality. However, the distribution and role of the lower respiratory tract (LRT) microbiome in patients with IIM-ILD remains unclear. This study aimed to investigate the microbial diversity and community differences in bronchoalveolar lavage fluid (BALF) in patients with IIM-ILD...
2024: Frontiers in Medicine
#39
REVIEW
Mari Murakami
Tissue-resident memory T cells (TRM ) serve as the frontline of host defense, playing a critical role in protection against invading pathogens. This emphasizes their role in providing rapid on-site immune responses across various organs. The physiological significance of TRM is not just confined to infection control; accumulating evidence has revealed that TRM also determine the pathology of diseases such as autoimmune disorders, inflammatory bowel disease, and cancer. Intensive studies on the origin, mechanisms of formation and maintenance, and physiological significance of TRM have elucidated the transcriptional and functional diversity of these cells, which are often affected by local cues associated with their presence...
April 17, 2024: Inflammation and Regeneration
#40
JOURNAL ARTICLE
Chihiro Mimura, Rei Takamiya, Shodai Fujimoto, Takafumi Fukui, Atsuhiko Yatani, Jun Yamada, Mizuki Takayasu, Naoya Takata, Hiroki Sato, Kiyoko Fukuda, Koichi Furukawa, Daisuke Hazama, Naoko Katsurada, Masatsugu Yamamoto, Shingo Matsumoto, Koichi Goto, Motoko Tachihara
BACKGROUND: Next-generation sequencing (NGS) is essential for lung cancer treatment. It is important to collect sufficient tissue specimens, but sometimes we cannot obtain large enough samples for NGS analysis. We investigated the yield of NGS analysis by frozen cytology pellets using an Oncomine Comprehensive Assay or Oncomine Precision Assay. METHODS: We retrospectively enrolled patients with lung cancer who underwent bronchoscopy at Kobe University Hospital and were enrolled in the Lung Cancer Genomic Screening Project for Individualized Medicine...
April 17, 2024: BMC Cancer
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