In this chapter, we describe methods for functional genomics studies in mouse macrophages. In particular, we describe complementary methods for gene inhibition using RNA interference (RNAi) and gene overexpression. These methods are readily amenable to medium- and high-throughput functional genomics investigations. These complementary loss-of-function and gain-of-function genomic approaches provide a rapid means of investigating the function of candidate genes prior to initiating more cumbersome studies in vivo.
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http://dx.doi.org/10.1007/978-1-4939-8570-8_18 | DOI Listing |
Clin Dysmorphol
January 2025
Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
Introduction: Agrin, encoded by AGRN, plays a vital role in the acetylcholine receptor clustering pathway, and any defects in this pathway are known to cause congenital myasthenic syndrome (CMS) 8 in early childhood with variable fatigable muscle weakness. The most severe or lethal form of CMS manifests as a fetal akinesia deformation sequence (FADS). To date, only one family has been reported with an association of null variants in AGRN and a lethal FADS.
View Article and Find Full Text PDFHeliyon
January 2025
Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary.
Heat stress has been proven to cause negative effects on livestock leading to lower productivity and economic value. Understanding how heat stress manifests within an animal's body is the first step in devising a heat stress mitigation strategy; transcriptomic studies are one of the methods used. Here, using a systematic literature review methodology, we examine the recent decade of transcriptomics' application to the study of livestock adaptation.
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January 2025
Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.
Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality.
View Article and Find Full Text PDFOncol Lett
March 2025
Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua 50006, Taiwan, ROC.
EGFR and ALK are key driver mutations in non-small cell lung cancer (NSCLC). Tyrosine kinase inhibitors are recommended as the first-line treatment for advanced NSCLC with driving oncogenes because they have fewer side effects and provide better disease control than chemotherapy. The present retrospective analysis aimed to investigate how altered driver genes impact cancer outcomes and clinical presentation.
View Article and Find Full Text PDFAPMIS
January 2025
Department of Laboratory Medicine, Clinical Microbiology Örebro University Hospital and Faculty of Medicine and Health at Örebro University, Örebro, Sweden.
Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation.
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