Methods in molecular biology (Clifton, N.J.)
Busman-Sahay, K;Nekorchuk, MD;Starke, CE;Chan, CN;Estes, JD;
PMID: 34985671 | DOI: 10.1007/978-1-0716-1871-4_19
Modern combination antiretroviral therapy (ART) regimens provide abiding viral suppression for most individuals infected with human immunodeficiency virus (HIV). However, the persistence of viral reservoirs ensures that eradication of HIV-1 (i.e., cure) or sustained ART-free remission (i.e., functional cure) remains elusive, necessitating continual, strict ART adherence and contributing to HIV-1-related comorbidities. Eradication of these viral reservoirs, which persist primarily within lymphoid tissue, will require a deeper understanding of the cellular neighborhoods in which latent and active HIV-1-infected cells reside. By pairing highly sensitive in situ hybridization (ISH) with an exceptionally flexible immunofluorescence (IF) approach, we describe a simple, yet highly adaptable multiplex protocol for investigating the quantity, distribution, and characteristics of HIV-1 viral reservoirs.
Biomarkers in Carcinoma of Unknown Primary
Talu, C;Ulukus, E;Zheng, W;
| DOI: 10.1007/978-3-030-84432-5_10
We use cookies to make sure that our website works properly, as well as some ‘optional’ cookies to personalise content and advertising, provide social media features and analyse how people use our site. By accepting some or all optional cookies you give consent to the processing of your personal data, including transfer to third parties, some in countries outside of the European Economic Area that do not offer the same data protection standards as the country where you live. You can decide which optional cookies to accept by clicking on ‘Manage Settings’, where you can also find more information about how your personal data is processed. Further information can be found in our privacy policy [https://link.springer.com/privacystatement].
Armwood, AR;Stilwell, JM;Ng, TFF;Clauss, TM;Leary, JH;Mader, D;Camus, AC;
PMID: 34794368 | DOI: 10.1177/03009858211052662
A juvenile, male tiger shark (Galeocerdo cuvier) developed illness after capture in Florida waters and was euthanized. Gross lesions included mild skin abrasions, hepatic atrophy, and coelomic fluid. Histologically, gills contained multifocal lamellar epithelial cell necrosis and thromboses. Scattered gill and esophageal epithelial cells had large, basophilic, intracytoplasmic, and intranuclear inclusions. Ultrastructurally, lamellar epithelial cells contained arrays of intracytoplasmic viral particles and scattered intranuclear nucleocapsids. Capsulated virions were 148 ± 11 nm with an 84 ± 8 nm icosahedral nucleocapsid and an electron-dense core. Next-generation sequencing, quantitative polymerase chain reaction, and in situ hybridization performed on formalin-fixed tissue confirmed a herpes-like viral infection. The viral polymerase shared 24% to 31% protein homology with other alloherpesviruses of fish, indicating a divergent virus. This report documents the pathologic findings associated with a molecularly confirmed novel herpes-like virus in an elasmobranch.
Single-cell omics: Overview, analysis, and application in biomedical science
Journal of cellular biochemistry
Stein, CM;Weiskirchen, R;Damm, F;Strzelecka, PM;
PMID: 34459502 | DOI: 10.1002/jcb.30134
Single-cell sequencing methods provide the highest resolution insight into cellular heterogeneity. Owing to their rapid growth and decreasing cost, they are now widely accessible to scientists worldwide. Single-cell technologies enable analysis of a large number of cells, making them powerful tools to characterise rare cell types and refine our understanding of diverse cell states. Moreover, single-cell application in biomedical sciences helps to unravel mechanisms related to disease pathogenesis and outcome. In this Viewpoint, we briefly describe existing single-cell methods (genomics, transcriptomics, epigenomics, proteomics, and mulitomics), comment on available analysis tools, and give examples of method applications in the biomedical field.
Cell-cell contact and signaling in the muscle stem cell niche
Current opinion in cell biology
Kann, AP;Hung, M;Krauss, RS;
PMID: 34352725 | DOI: 10.1016/j.ceb.2021.06.003
Muscle stem cells (also called satellite cells or SCs) rely on their local niche for regulatory signals during homeostasis and regeneration. While a number of cell types communicate indirectly through secreted factors, here we focus on the significance of direct contact between SCs and their neighbors. During quiescence, SCs reside under a basal lamina and receive quiescence-promoting signals from their adjacent skeletal myofibers. Upon injury, the composition of the niche changes substantially, enabling the formation of new contacts that mediate proliferation, self-renewal, and differentiation. In this review, we summarize the latest work in understanding cell-cell contact within the satellite cell niche and highlight areas of open questions for future studies.
Transcriptional and Anatomical Diversity of Medium Spiny Neurons in the Primate Striatum
He, J;Kleyman, M;Chen, J;Alikaya, A;Rothenhoefer, K;Ozturk, B;Wirthlin, M;Fish, K;Byrne, L;Pfenning, A;Stauffer, W;
| DOI: 10.2139/ssrn.3815985
The striatum is the interface between dopamine reward signals and cortico-basal ganglia circuits that mediate diverse behavioral functions. Medium spiny neurons (MSNs) constitute the vast majority of striatal neurons and are traditionally classified as direct- or indirect-pathway neurons. However, that traditional model does not explain the anatomical and functional diversity of MSNs. Here, we defined molecularly distinct MSN types in the primate striatum, including (1) dorsal striatum MSN types associated with striosome and matrix compartments, (2) ventral striatum types associated with the nucleus accumbens shell and olfactory tubercle, and (3) an MSN-like type restricted to μ-opioid receptor rich islands in the ventral striatum. These results lay the foundation for achieving cell type-specific transgenesis in the primate striatum and provide a blueprint for investigating circuit-specific processing.
Single-cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs
Genes, chromosomes & cancer
Pfisterer, U;Bräunig, J;Brattås, P;Heidenblad, M;Karlsson, G;Fioretos, T;
PMID: 33611828 | DOI: 10.1002/gcc.22944
The ability to capture alterations in the genome or transcriptome by next-generation sequencing has provided critical insight into molecular changes and programs underlying cancer biology. With the rapid technological development in single-cell sequencing, it has become possible to study individual cells at the transcriptional, genetic, epigenetic, and protein level. Using single-cell analysis, an increased resolution of fundamental processes underlying cancer development is obtained, providing comprehensive insights otherwise lost by sequencing of entire (bulk) samples, in which molecular signatures of individual cells are averaged across the entire cell population. Here, we provide a concise overview on the application of single-cell analysis of different modalities within cancer research by highlighting key articles of their respective fields. We furthermore examine the potential of existing technologies to meet clinical diagnostic needs and discuss current challenges associated with this translation. This article is protected by
Soh H, Park S, Ryan K, Springer K, Maheshwari A, Tzingounis AV.
PMID: 30382937 | DOI: 10.7554/eLife.38617
KCNQ2/3 channels, ubiquitously expressed neuronal potassium channels, have emerged as indispensable regulators of brain network activity. Despite their critical role in brain homeostasis, the mechanisms by which KCNQ2/3 dysfunction lead to hypersychrony are not fully known. Here, we show that deletion of KCNQ2/3 channels changed PV+ interneurons', but not SST+ interneurons', firing properties. We also find that deletion of either KCNQ2/3 or KCNQ2 channels from PV+ interneurons led to elevated homeostatic potentiation of fast excitatory transmission in pyramidal neurons. Pvalb-Kcnq2 null-mice showed increased seizure susceptibility, suggesting that decreases in interneuron KCNQ2/3 activity remodels excitatory networks, providing a new function for these channels.
Genetic Engineering & Biotechnology News
LeMieux, J;
| DOI: 10.1089/gen.43.06.13
A patient's genome, Van Eyk noted, contains information about that patient's disease predispositions and drug responses. She added, however, that better information about disease risks and drug responses could be gleaned from the proteome. Although there are only so many protein-encoding genes, the intricacies of protein expression generate various kinds of proteomic information in abundance. According to Van Eyk, information about disease-induced modifications, isoforms, concentration changes, and chemical complexity can inform predictions of what will happen in the body, in the context of the body and the environment. She suggests that a proteomics approach—one that would involve monitoring of not just one protein at a time, but thousands—could generate valuable clinical insights.
Roy, AL;Conroy, RS;Taylor, VG;Mietz, J;Fingerman, IM;Pazin, MJ;Smith, P;Hutter, CM;Singer, DS;Wilder, EL;
PMID: 36640770 | DOI: 10.1016/j.molcel.2022.12.025
Genomic architecture appears to play crucial roles in health and a variety of diseases. How nuclear structures reorganize over different timescales is elusive, partly because the tools needed to probe and perturb them are not as advanced as needed by the field. To fill this gap, the National Institutes of Health Common Fund started a program in 2015, called the 4D Nucleome (4DN), with the goal of developing and ultimately applying technologies to interrogate the structure and function of nuclear organization in space and time.
Cui, Y;Zhang, X;Li, X;Lin, J;
PMID: 36477856 | DOI: 10.1111/nph.18641
New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.
Ben Aribi, H;Ding, M;Kiran, A;
| DOI: 10.12688/f1000research.126840.1
Background: The identification of differentially expressed genes and their associated biological processes, molecular function, and cellular components are important for genetic diseases studies because they present potential biomarkers and therapeutic targets. Methods: In this study, we developed an o²S²PARC template representing an interactive pipeline for the gene expression data visualization and ontologies data analysis and visualization. To demonstrate the usefulness of the tool, we performed a case study on a publicly available dataset. Results: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. The ontologies associated with the DEGs are determined and visualized in barplots. Conclusions: The “Expression data visualization” template is publicly available on the o²S²PARC platform.
