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JOURNAL ARTICLE
Rumie Matsumura, Gaku Sato, Yutetsu Kuruma
Phospholipids are important biomolecules for the study of lipidomics, signal transduction, biodiesel, and synthetic biology; however, it is difficult to synthesize and analyze phospholipids in a defined in vitro condition. Here, we present a protocol for in vitro production and quantification of phospholipids. We describe steps for preparing a cell-free system consisting of fatty acid synthesis and a gene expression system that synthesizes acyltransferases on liposomes. The whole reaction can be completed within a day and the products are quantified by liquid chromatography-mass spectrometry...
May 2, 2024: STAR protocols
#22
JOURNAL ARTICLE
Arya Y Nakhe, Prasanna K Dadi, Jinsun Kim, Matthew T Dickerson, Soma Behera, Jordyn R Dobson, Shristi Shrestha, Jean-Philippe Cartailler, Leesa Sampson, Mark A Magnuson, David A Jacobson
The gain-of-function mutation in the TALK-1 K+ channel (p.L114P) is associated with maturity-onset diabetes of the young (MODY). TALK-1 is a key regulator of β-cell electrical activity and glucose-stimulated insulin secretion. The KCNK16 gene encoding TALK-1 is the most abundant and β-cell-restricted K+ channel transcript. To investigate the impact of KCNK16 L114P on glucose homeostasis and confirm its association with MODY, a mouse model containing the Kcnk16 L114P mutation was generated. Heterozygous and homozygous Kcnk16 L114P mice exhibit increased neonatal lethality in the C57BL/6J and the CD-1 (ICR) genetic background, respectively...
May 3, 2024: ELife
#23
COMPARATIVE STUDY
Yuto Fukuda, Yuka Torii, Ken-Ichi Iwata, Kazunori Haruta, Makoto Yamaguchi, Takako Suzuki, Atsushi Narita, Hideki Muramatsu, Yasuhiro Ogura, Yoshiyuki Takahashi, Yoshinori Ito, Jun-Ichi Kawada
Monitoring Epstein-Barr virus (EBV) and cytomegalovirus (CMV) infection after transplantation is recommended to enable preemptive therapy. However, the most suitable sample type remains unclear. Patients who underwent hematopoietic stem cell or liver transplantation were included in this study. Viral loads in sequential whole-blood and plasma samples were retrospectively analyzed. EBV DNA was detected more frequently in whole blood (55%) than in plasma (18%). The detection rate of CMV DNA was similar between the two sample types...
May 2024: New Microbiologica
#24
JOURNAL ARTICLE
A A Soldatov, N E Shalagina, V N Rychkova, T A Kukhareva
The content of membrane-bound methemoglobin (MtHb) in nucleated erythrocytes was studied in the black scorpionfish Scorpaena porcus (Linnaeus, 1758) in vitro. Spectral characteristics were determined for a whole hemolysate, a hemolysate obtained by stroma precipitation (a clarified hemolysate), and a resuspended stroma. The MtHb proportion in the erythrocyte stroma was found to exceed 80% (6.20 ± 0.59 µM). Clarified hemolysates were nearly free of MtHb (0.5 ± 0.2 µM). Membrane-bound ferric hemoglobin did not affect the erythrocyte resistance to osmotic shock...
May 3, 2024: Doklady Biological Sciences: Proceedings of the Academy of Sciences of the USSR, Biological Sciences Sections
#25
JOURNAL ARTICLE
Mei-Fang Zhao, Song-Lin Zhang, YangZiYu Xiang, Qian Wang, Gao-Hui Cao, Ping-Ping Zhang, Liang-Liang Fan, Rong Yu, Ya-Li Li
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome (MPPH), a type of overgrowth syndrome, is characterized by progressive megalencephaly, cortical brain malformations, and distal limb anomalies. Previous studies have revealed that the overactivity of the phosphatidylinositol 3-kinase-Protein kinase B pathway and the increased cyclin D2 (CCND2) expression were the main factors contributing to this disease. Here, we present the case of a patient who exhibited megalencephaly, polymicrogyria, abnormal neuronal migration, and developmental delay...
May 3, 2024: DNA and Cell Biology
#26
JOURNAL ARTICLE
Shengfeng Ruan, Christina R Bourne
UNLABELLED: Plasmids play important roles in microbial ecosystems, serving as carriers of antibiotic resistance and virulence. In the laboratory, they are essential tools for genetic manipulation and recombinant protein expression. We uncovered an intriguing survival phenotype in a fraction of the bacterial population while using plasmid-mediated arabinose-inducible gene expression to monitor the production of toxic ParE proteins. This phenotype was not correlated with changes to the plasmid sequence and could not be rescued by increasing arabinose uptake...
May 3, 2024: Microbiology Spectrum
#27
JOURNAL ARTICLE
Nathan Bulangalire, Charlotte Claeyssen, Sana Douffi, Onnik Agbulut, Caroline Cieniewski-Bernard
Post-translational modifications (PTMs), such as phosphorylation and O-N-acetyl-β-d-glucosaminylation (O-GlcNAcylation), are involved in the fine spatiotemporal regulation of protein functions, and their dynamic interplay is at the heart of protein language. The coexistence of phosphorylation and O-GlcNAcylation on a protein leads to the diversification of proteoforms. It is therefore essential to decipher the phosphorylation/O-GlcNAcylation interplay on protein species that orchestrates cellular processes in a specific physiological or pathophysiological context...
May 3, 2024: Electrophoresis
#28
JOURNAL ARTICLE
M Adelita Vizcaino, Caterina Giannini, Daniel Lalich, Ali Nael, Robert B Jenkins, Quynh Tran, Brent A Orr, Zied Abdullaev, Kenneth Aldape, Rachael A Vaubel
Ganglioglioma (GG) with anaplasia (anaplastic ganglioglioma) is a rare and controversial diagnosis. When present, anaplasia involves the glial component of the tumor, either at presentation or at recurrence. To date, most published cases lack molecular characterization. We describe the histologic and molecular features of 3 patients presenting with BRAF p. V600E-mutant GG (CNS WHO grade 1) with high-grade glial transformation at recurrence. The tumors occurred in pediatric patients (age 9-16 years) with time to recurrence from 20 months to 7 years...
May 2, 2024: Journal of Neuropathology and Experimental Neurology
#29
JOURNAL ARTICLE
Chidiebere U Awah, Joo Sun Mun, Aloka Paragodaarachchi, Baris Boylu, Martin Nzegwu, Hiroshi Matsui, Olorunseun Ogunwobi
Non-small cell lung cancer (NSCLC) caused more deaths in 2017 than breast cancer, prostate, and brain cancers combined. This is primarily due to their aggressive metastatic nature, leading to more fatal rates of cancer patients. Despite this condition, there are no clinically approved drugs that can target metastasis. The NSCLC with EGFR T790M-overexpressing HER2 shows the resistance to osimertinib and trastuzumab starting 10-18 months after the therapy, and thus prospects are grim to these patients. To target the recalcitrant ERBB2 driver oncogene, we developed two engineered destabilizing 3'UTR ERBB2 constructs that degrade the endogenous ERBB2 transcript and proteins by overwriting the encoded endogenous ERBB2 mRNA with the destabilizing message...
2024: Frontiers in Oncology
#30
JOURNAL ARTICLE
Wenjing Liu, Xiaoxiang Hu, Yi Yan, Yujie Cai
Spermidine is a naturally occurring polyamine widely utilized in the prevention and treatment of various diseases. Current spermidine biosynthetic methods have problems such as low efficiency and complex multi-enzyme catalysis. Based on sequence-structure-function relationships, we engineered the widely studied homospermidine synthase from Blastochloris viridis ( Bv HSS) and obtained mutants that could catalyze the production of spermidine from 1,3-diaminopropane and putrescine. The specific activities of Bv HSS and the mutants D361E and E232D + D361E (E232D-D) were 8...
September 2024: Synthetic and Systems Biotechnology
#31
REVIEW
Nesrine Lajmi, Sofia Alves-Vasconcelos, Apostolos Tsiachristas, Andrew Haworth, Kerrie Woods, Charles Crichton, Theresa Noble, Hizni Salih, Kinga A Várnai, Harriet Branford-White, Liam Orrell, Andrew Osman, Kevin M Bradley, Lara Bonney, Daniel R McGowan, Jim Davies, Matthew S Prime, Andrew Bassim Hassan
The personalised oncology paradigm remains challenging to deliver despite technological advances in genomics-based identification of actionable variants combined with the increasing focus of drug development on these specific targets. To ensure we continue to build concerted momentum to improve outcomes across all cancer types, financial, technological and operational barriers need to be addressed. For example, complete integration and certification of the 'molecular tumour board' into 'standard of care' ensures a unified clinical decision pathway that both counteracts fragmentation and is the cornerstone of evidence-based delivery inside and outside of a research setting...
2024: Camb Prism Precis Med
#32
JOURNAL ARTICLE
Mizuho Kittaka, Noriyoshi Mizuno, Hiroyuki Morino, Tetsuya Yoshimoto, Tianli Zhu, Sheng Liu, Ziyi Wang, Kotoe Mayahara, Kyohei Iio, Kaori Kondo, Toshio Kondo, Tatsuhide Hayashi, Sarah Coghlan, Yayoi Teno, Andrew Anh Phung Doan, Marcus Levitan, Roy B Choi, Shinji Matsuda, Kazuhisa Ouhara, Jun Wan, Annelise M Cassidy, Stephane Pelletier, Sheela Nampoothiri, Andoni J Urtizberea, Alexander G Robling, Mitsuaki Ono, Hideshi Kawakami, Ernst J Reichenberger, Yasuyoshi Ueki
Cherubism (OMIM 118400) is a rare craniofacial disorder in children characterized by destructive jawbone expansion due to the growth of inflammatory fibrous lesions. Our previous studies have shown that gain-of-function mutations in SH3 domain-binding protein 2 (SH3BP2) are responsible for cherubism and that a knock-in mouse model for cherubism recapitulates the features of cherubism, such as increased osteoclast formation and jawbone destruction. To date, SH3BP2 is the only gene identified to be responsible for cherubism...
June 2024: JBMR Plus
#33
JOURNAL ARTICLE
Andrei Kudriavtsev, Brice Pastor, Alexia Mirandola, Ekaterina Pisareva, Yann Gricourt, Xavier Capdevila, Alain R Thierry, Philippe Cuvillon
OBJECTIVES: Elevated circulating DNA (cirDNA) concentrations were found to be associated with trauma or tissue damage which suggests involvement of inflammation or cell death in post-operative cirDNA release. We carried out the first prospective, multicenter study of the dynamics of cirDNA and neutrophil extracellular trap (NETs) markers during the perioperative period from 24 h before surgery up to 72 h after curative surgery in cancer patients. METHODS: We examined the plasma levels of two NETs protein markers [myeloperoxidase (MPO) and neutrophil elastase (NE)], as well as levels of cirDNA of nuclear (cir-nDNA) and mitochondrial (cir-mtDNA) origin in 29 colon, prostate, and breast cancer patients and in 114 healthy individuals (HI)...
June 2024: Precision Clinical Medicine
#34
Yujin Kim, Minwoo Jeong, In Gyeong Koh, Chanhee Kim, Hyeji Lee, Jae Hyun Kim, Ronald Yurko, Il Bin Kim, Jeongbin Park, Donna M Werling, Stephan J Sanders, Joon-Yong An
UNLABELLED: Variants in cis-regulatory elements link the noncoding genome to human brain pathology; however, detailed analytic tools for understanding the association between cell-level brain pathology and noncoding variants are lacking. CWAS-Plus, adapted from a Python package for category-wide association testing (CWAS) employs both whole-genome sequencing and user-provided functional data to enhance noncoding variant analysis, with a faster and more efficient execution of the CWAS workflow...
April 15, 2024: medRxiv
#35
Laura Torrens, Sarah Moody, Ana Carolina de Carvalho, Mariya Kazachkova, Behnoush Abedi-Ardekani, Saamin Cheema, Sergey Senkin, Thomas Cattiaux, Ricardo Cortez Cardoso Penha, Joshua R Atkins, Valérie Gaborieau, Priscilia Chopard, Christine Carreira, Ammal Abbasi, Erik N Bergstrom, Raviteja Vangara, Jingwei Wang, Stephen Fitzgerald, Calli Latimer, Marcos Diaz-Gay, David Jones, Jon Teague, Felipe Ribeiro Pinto, Luiz Paulo Kowalski, Jerry Polesel, Fabiola Giudici, José Carlos de Oliveira, Pagona Lagiou, Areti Lagiou, Marta Vilensky, Dana Mates, Ioan N Mates, Lidia Mrb Arantes, Rui Reis, Jose Roberto V Podesta, Sandra V von Zeidler, Ivana Holcatova, Maria Paula Curado, Cristina Canova, Elenora Fabianova, Paula A Rodríguez-Urrego, Laura Humphreys, Ludmil B Alexandrov, Paul Brennan, Michael R Stratton, Sandra Perdomo
Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). Here, we further explore how tobacco exposure contributes to cancer development by mutational signature analysis of 265 whole-genome sequenced HNC from eight countries. Six tobacco-associated mutational signatures were detected, including some not previously reported. Differences in HNC incidence between countries corresponded with differences in mutation burdens of tobacco-associated signatures, consistent with the dominant role of tobacco in HNC causation...
April 17, 2024: medRxiv
#36
Yasminka A Jakubek, Xiaolong Ma, Adrienne M Stilp, Fulong Yu, Jason Bacon, Justin W Wong, Francois Aguet, Kristin Ardlie, Donna Arnett, Kathleen Barnes, Joshua C Bis, Tom Blackwell, Lewis C Becker, Eric Boerwinkle, Russell P Bowler, Matthew J Budoff, April P Carson, Jiawen Chen, Michael H Cho, Josef Coresh, Nancy Cox, Paul S de Vries, Dawn L DeMeo, David W Fardo, Myriam Fornage, Xiuqing Guo, Michael E Hall, Nancy Heard-Costa, Bertha Hidalgo, Marguerite Ryan Irvin, Andrew D Johnson, Eimear E Kenny, Dan Levy, Yun Li, Joao Ac Lima, Yongmei Liu, Ruth J F Loos, Mitchell J Machiela, Rasika A Mathias, Braxton D Mitchell, Joanne Murabito, Josyf C Mychaleckyj, Kari North, Peter Orchard, Stephen Cj Parker, Yash Pershad, Patricia A Peyser, Katherine A Pratte, Bruce M Psaty, Laura M Raffield, Susan Redline, Stephen S Rich, Jerome I Rotter, Sanjiv J Shah, Jennifer A Smith, Aaron P Smith, Albert Smith, Margaret Taub, Hemant K Tiwari, Russell Tracy, Bjoernar Tuftin, Alexander G Bick, Vijay G Sankaran, Alexander P Reiner, Paul Scheet, Paul L Auer
Mosaic loss of Y (mLOY) is the most common somatic chromosomal alteration detected in human blood. The presence of mLOY is associated with altered blood cell counts and increased risk of Alzheimer's disease, solid tumors, and other age-related diseases. We sought to gain a better understanding of genetic drivers and associated phenotypes of mLOY through analyses of whole genome sequencing of a large set of genetically diverse males from the Trans-Omics for Precision Medicine (TOPMed) program. This approach enabled us to identify differences in mLOY frequencies across populations defined by genetic similarity, revealing a higher frequency of mLOY in the European American (EA) ancestry group compared to those of Hispanic American (HA), African American (AA), and East Asian (EAS) ancestry...
April 19, 2024: medRxiv
#37
Omar Nadeem, Michelle P Aranha, Robert Redd, Michael Timonian, Sophie Magidson, Elizabeth D Lightbody, Jean-Baptiste Alberge, Luca Bertamini, Ankit K Dutta, Habib El-Khoury, Mark Bustoros, Jacob P Laubach, Giada Bianchi, Elizabeth O'Donnell, Ting Wu, Junko Tsuji, Kenneth Anderson, Gad Getz, Lorenzo Trippa, Paul G Richardson, Romanos Sklavenitis-Pistofidis, Irene M Ghobrial
BACKGROUND: Early therapeutic intervention in high-risk SMM (HR-SMM) has demonstrated benefit in previous studies of lenalidomide with or without dexamethasone. Triplets and quadruplet studies have been examined in this same population. However, to date, none of these studies examined the impact of depth of response on long-term outcomes of participants treated with lenalidomide-based therapy, and whether the use of the 20/2/20 model or the addition of genomic alterations can further define the population that would benefit the most from early therapeutic intervention...
April 19, 2024: medRxiv
#38
JOURNAL ARTICLE
Simin Cheng, Chenxi Cao, Yao Qian, Huan Yao, Xiaoyun Gong, Xinhua Dai, Zheng Ouyang, Xiaoxiao Ma
Single-cell mass spectrometry (MS) is an essential technology for sensitive and multiplexed analysis of metabolites and lipids for cell phenotyping and pathway studies. However, the structural elucidation of lipids from single cells remains a challenge, especially in the high-throughput scenario. Technically, there is a contradiction between the inadequate sample amount ( i.e. a single cell, 0.5-20 pL) for replicate or multiple analysis, on the one hand, and the high metabolite coverage and multidimensional structure analysis that needs to be performed for each single cell, on the other hand...
May 1, 2024: Chemical Science
#39
JOURNAL ARTICLE
Helene Babski, Marcello Codianni, Vikas Bhandawat
Projection neurons that communicate between different brain regions and local neurons that shape computation within a brain region form the majority of all neurons in the brain. Another important class of neurons is neuromodulatory neurons; these neurons are in much smaller numbers than projection/local neurons but have a large influence on computations in the brain. Neuromodulatory neurons are classified by the neurotransmitters they carry, such as dopamine and serotonin. Much of our knowledge of the effect of neuromodulators comes from experiments in which either a large population of neuromodulatory neurons or the entire population is perturbed...
May 15, 2024: Heliyon
#40
JOURNAL ARTICLE
Hubert Bernauer, Anja Schlör, Josef Maier, Katja Hanack, Norbert Bannert, Daniel Ivanusic
Monitoring specific antibodies derived from whole-cell immunization through cell-based ELISA methods poses challenges due to humoral responses against various cell proteins. In this report, we outline a technique involving pre-adsorption on cells to remove undesirable antibodies from immune serum. This step provides the subsequent monitoring of antibodies specific to the targeted antigen using a tANCHOR-based ELISA. Notably, this approach accelerates result acquisition, eliminating the necessity to purify the expressed antigen or obtain a customized peptide for coating assay plates...
2024: microPublication. Biology
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