Comparative Bioinformatic Analysis of the Proteomes of Rabbit and Human Sex Chromosomes
Animals (Basel). 2024 Jan 9;14(2):217. doi: 10.3390/ani14020217.ABSTRACTStudying proteins associated with sex chromosomes can provide insights into sex-specific proteins. Membrane proteins accessible through the cell surface may serve as excellent targets for diagnostic, therapeutic, or even technological purposes, such as sperm sexing technologies. In this context, proteins encoded by sex chromosomes have the potential to become targets for X- or Y-chromosome-bearing spermatozoa. Due to the limited availability of proteomic studies on rabbit spermatozoa and poorly annotated databases for rabbits compared to humans, a bioi...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Patr ícia Pinto-Pinho Jo ão Soares Pedro Esteves Ros ário Pinto-Leite Margarida Fardilha Bruno Cola ço Source Type: research
Omics Studies of Tumor Cells under Microgravity Conditions
Int J Mol Sci. 2024 Jan 11;25(2):926. doi: 10.3390/ijms25020926.ABSTRACTCancer is defined as a group of diseases characterized by abnormal cell growth, expansion, and progression with metastasis. Various signaling pathways are involved in its development. Malignant tumors exhibit a high morbidity and mortality. Cancer research increased our knowledge about some of the underlying mechanisms, but to this day, our understanding of this disease is unclear. High throughput omics technology and bioinformatics were successful in detecting some of the unknown cancer mechanisms. However, novel groundbreaking research and ideas are ...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Jenny Graf Herbert Schulz Markus Wehland Thomas J Corydon Jayashree Sahana Fatima Abdelfattah Simon L Wuest Marcel Egli Marcus Kr üger Armin Kraus Petra M Wise Manfred Infanger Daniela Grimm Source Type: research
Investigating the Potential Shared Molecular Mechanisms between COVID-19 and Alzheimer's Disease via Transcriptomic Analysis
Viruses. 2024 Jan 9;16(1):100. doi: 10.3390/v16010100.ABSTRACTSARS-CoV-2 caused the COVID-19 pandemic. COVID-19 may elevate the risk of cognitive impairment and even cause dementia in infected individuals; it may accelerate cognitive decline in elderly patients with dementia, possibly in Alzheimer's disease (AD) patients. However, the mechanisms underlying the interplay between AD and COVID-19 are still unclear. To investigate the underlying mechanisms and associations between AD progression and SARS-CoV-2 infection, we conducted a series of bioinformatics research into SARS-CoV-2-infected cells, COVID-19 patients, AD pati...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Yixian Fan Xiaozhao Liu Fei Guan Xiaoyi Hang Ximiao He Jing Jin Source Type: research
Large language models in bioinformatics: applications and perspectives
ArXiv. 2024 Jan 8:arXiv:2401.04155v1. Preprint.ABSTRACTLarge language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of unlabeled input using self-supervised or semi-supervised learning. However, their potential for solving bioinformatics problems may even exceed their proficiency in modeling human language. In this review, we will present a summary of the prominent large l...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Jiajia Liu Mengyuan Yang Yankai Yu Haixia Xu Kang Li Xiaobo Zhou Source Type: research
Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops
Front Plant Sci. 2024 Jan 8;14:1273859. doi: 10.3389/fpls.2023.1273859. eCollection 2023.ABSTRACTThe deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop ...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Rubab Zahra Naqvi Muhammad Arslan Mahmood Shahid Mansoor Imran Amin Muhammad Asif Source Type: research
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity
bioRxiv. 2024 Jan 16:2024.01.07.574538. doi: 10.1101/2024.01.07.574538. Preprint.ABSTRACTNeuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic metho...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Anand G Patel Orr Ashenberg Natalie B Collins Åsa Segerstolpe Sizun Jiang Michal Slyper Xin Huang Chiara Caraccio Hongjian Jin Heather Sheppard Ke Xu Ti-Cheng Chang Brent A Orr Abbas Shirinifard Richard H Chapple Amber Shen Michael R Clay Ruth G Tatevoss Source Type: research
Reprogramming neuroblastoma by diet-enhanced polyamine depletion
bioRxiv. 2024 Jan 8:2024.01.07.573662. doi: 10.1101/2024.01.07.573662. Preprint.ABSTRACTNeuroblastoma is a highly lethal childhood tumor derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fueled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, with the inhibitor difluoromethylornithine showing clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumor differentiation, and p...
Source: Genomics Proteomics ... - January 23, 2024 Category: Genetics & Stem Cells Authors: Sarah Cherkaoui Lifeng Yang Matthew McBride Christina S Turn Wenyun Lu Caroline Eigenmann George E Allen Olesya O Panasenko Lu Zhang Annette Vu Kangning Liu Yimei Li Om H Gandhi Lea Surrey Michael Wierer Eileen White Joshua D Rabinowitz Michael D Hogarty Source Type: research
Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat
Plant Genome. 2024 Jan 18:e20427. doi: 10.1002/tpg2.20427. Online ahead of print.ABSTRACTBuckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological...
Source: Genomics Proteomics ... - January 19, 2024 Category: Genetics & Stem Cells Authors: Samiullah Naik Jebi Sudan Uneeb Urwat Mohammad Maqbool Pakhtoon Basharat Bhat Varun Sharma Parvaze A Sofi Asif B Shikari Bilal A Bhat Najeebul Rehman Sofi P V Vara Prasad Sajad Majeed Zargar Source Type: research
Ribosome inactivation regulates translation elongation in neurons
In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by ...
Source: Genomics Proteomics ... - January 14, 2024 Category: Genetics & Stem Cells Authors: Bastian Popper Martina B ürkle Giuliana Ciccopiedi Marta Marchioretto Ignasi Forn é Axel Imhof Tobias Straub Gabriella Viero Magdalena G ötz Rico Schieweck Source Type: research
Proteomics and genomics insights on malignant osteosarcoma
Adv Protein Chem Struct Biol. 2024;138:275-300. doi: 10.1016/bs.apcsb.2023.06.001. Epub 2023 Nov 28.ABSTRACTOsteosarcoma is a malignant osseous neoplasm. Osteosarcoma is a primary bone malignancy capable of producing osteoid tissue or immature bones. A subsequent malignant degeneration of the primary bone pathology occurs less frequently in adults. The over-expression of several proteins, including Heat shock proteins, Cofilin, Annexins, Insulin-like growth factor, transforming growth factor-β, Receptor tyrosine kinase, Ezrin, Runx2, SATB2, ATF4, Annexins, cofilin, EGFR, VEGF, retinoblastoma 1 (Rb1) and secreted protein, ...
Source: Genomics Proteomics ... - January 14, 2024 Category: Genetics & Stem Cells Authors: Nachammai Kathiresan Chandrabose Selvaraj Sangavi Pandian Gowtham Kumar Subbaraj Abdulaziz S Alothaim Sher Zaman Safi Langeswaran Kulathaivel Source Type: research
Non-apoptotic FAS signaling controls mTOR activation and extrafollicular maturation in human B cells
Sci Immunol. 2024 Jan 12;9(91):eadj5948. doi: 10.1126/sciimmunol.adj5948. Epub 2024 Jan 12.ABSTRACTDefective FAS (CD95/Apo-1/TNFRSF6) signaling causes autoimmune lymphoproliferative syndrome (ALPS). Hypergammaglobulinemia is a common feature in ALPS with FAS mutations (ALPS-FAS), but paradoxically, fewer conventional memory cells differentiate from FAS-expressing germinal center (GC) B cells. Resistance to FAS-induced apoptosis does not explain this phenotype. We tested the hypothesis that defective non-apoptotic FAS signaling may contribute to impaired B cell differentiation in ALPS. We analyzed secondary lymphoid organs ...
Source: Genomics Proteomics ... - January 12, 2024 Category: Genetics & Stem Cells Authors: Julian Staniek Tomas Kalina Geoffroy Andrieux Melanie Boerries Iga Janowska Manuel Fuentes Paula D íez Marina Bakardjieva Jitka Stancikova Jan Raabe Julika Neumann Sabine Schwenk Leonardo Arpesella Jan Stuchly Vladimir Benes Rodrigo Garc ía Valiente Jon Source Type: research
Correction to: Disrupted hypothalamic transcriptomics and proteomics in a mouse model of type 2 diabetes exposed to recurrent hypoglycaemia
Diabetologia. 2024 Feb;67(2):403. doi: 10.1007/s00125-023-06083-3.NO ABSTRACTPMID:38206364 | PMC:PMC10789660 | DOI:10.1007/s00125-023-06083-3 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 11, 2024 Category: Genetics & Stem Cells Authors: Judit Castillo-Armengol Flavia Marzetta Ana Rodriguez Sanchez-Archidona Christian Fledelius Mark Evans Alison McNeilly Rory J McCrimmon Mark Ibberson Bernard Thorens Source Type: research
Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer
Cancer Cell. 2024 Jan 8;42(1):70-84.e8. doi: 10.1016/j.ccell.2023.12.012.ABSTRACTStrategies are needed to better identify patients that will benefit from immunotherapy alone or who may require additional therapies like chemotherapy or radiotherapy to overcome resistance. Here we employ single-cell transcriptomics and spatial proteomics to profile triple negative breast cancer biopsies taken at baseline, after one cycle of pembrolizumab, and after a second cycle of pembrolizumab given with radiotherapy. Non-responders lack immune infiltrate before and after therapy and exhibit minimal therapy-induced immune changes. Respond...
Source: Genomics Proteomics ... - January 9, 2024 Category: Genetics & Stem Cells Authors: Stephen L Shiao Kenneth H Gouin Nathan Ing Alice Ho Reva Basho Aagam Shah Richard H Mebane David Zitser Andrew Martinez Natalie-Ya Mevises Bassem Ben-Cheikh Regina Henson Monica Mita Philomena McAndrew Scott Karlan Armando Giuliano Alice Chung Farin Amers Source Type: research
Cerebrospinal fluid proteomics in patients with Alzheimer's disease reveals five molecular subtypes with distinct genetic risk profiles
Nat Aging. 2024 Jan;4(1):33-47. doi: 10.1038/s43587-023-00550-7. Epub 2024 Jan 9.ABSTRACTAlzheimer's disease (AD) is heterogenous at the molecular level. Understanding this heterogeneity is critical for AD drug development. Here we define AD molecular subtypes using mass spectrometry proteomics in cerebrospinal fluid, based on 1,058 proteins, with different levels in individuals with AD (n = 419) compared to controls (n = 187). These AD subtypes had alterations in protein levels that were associated with distinct molecular processes: subtype 1 was characterized by proteins related to neuronal hyperplasticity; subtype 2 by ...
Source: Genomics Proteomics ... - January 9, 2024 Category: Genetics & Stem Cells Authors: Betty M Tijms Ellen M Vromen Olav Mjaavatten Henne Holstege Lianne M Reus Sven van der Lee Kirsten E J Wesenhagen Luigi Lorenzini Lisa Vermunt Vikram Venkatraghavan Niccol ó Tesi Jori Tomassen Anouk den Braber Julie Goossens Eugeen Vanmechelen Frederik B Source Type: research
From beer to breadboards: yeast as a force for biological innovation
Genome Biol. 2024 Jan 4;25(1):10. doi: 10.1186/s13059-023-03156-9.ABSTRACTThe history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Seve...
Source: Genomics Proteomics ... - January 4, 2024 Category: Genetics & Stem Cells Authors: Hamid Kian Gaikani Monika Stolar Divya Kriti Corey Nislow Guri Giaever Source Type: research
