Biology Methods and Protocols最新文献

{"title":"Microcosmos explorers: foldscope workshop for science outreach in Mexican schools.","authors":"Samantha López Clinton","doi":"10.1093/biomethods/bpad035","DOIUrl":"10.1093/biomethods/bpad035","url":null,"abstract":"<p><p>Foldscopes are ultra-low-cost paper microscopes invented by Manu Prakash and Jim Cybulski at Stanford University. They are about as light as a pencil and waterproof, all whilst offering similar optic quality to traditional microscopes. Foldscopes do not require electricity or glass slides to be used, which increases the possibilities of their use in education and outreach activities with children or people with disabilities. In 2019, thanks to a material grant of 100 foldscopes from One World Science and additional purchased foldscopes, I designed and implemented a science workshop called <i>Exploradores del Microcosmos</i>, or Explorers of Microcosmos in English. The aim of the workshop was to help make microscopy more accessible, in particular at underfunded schools, and stimulate active learning about ecosystems and evolution in the participants. Within this article, I describe the workshop and relay my personal insights and reflections on its execution across multiple schools and groups in Mexico.</p>","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"8 1","pages":"bpad035"},"PeriodicalIF":3.6,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10759293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139088898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crowdsourcing Temporal Transcriptomic Coronavirus Host Infection Data: resources, guide, and novel insights","authors":"James Flynn, Mehdi M Ahmadi, Chase T McFarland, Michael D Kubal, Mark A Taylor, Zhang Cheng, Enrique C Torchia, Michael G Edwards","doi":"10.1093/biomethods/bpad033","DOIUrl":"https://doi.org/10.1093/biomethods/bpad033","url":null,"abstract":"Abstract The emergence of SARS-CoV-2 reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of COVID-19 during the pandemic. This study coupled existing transcriptomic data from SARS-CoV-1 lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g., CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA Damage Response and Repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients that died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"102 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134957760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methods for Studying Mammalian Aquaporin Biology","authors":"Shohini Banerjee, Ian M Smith, Autumn C Hengen, Kimberly M Stroka","doi":"10.1093/biomethods/bpad031","DOIUrl":"https://doi.org/10.1093/biomethods/bpad031","url":null,"abstract":"Abstract Aquaporins (AQPs), transmembrane water-conducting channels, have earned a great deal of scrutiny for their critical physiological roles in healthy and disease cell states, especially in the biomedical field. Numerous methods have been implemented to elucidate the involvement of AQP-mediated water transport and downstream signaling activation in eliciting whole cell, tissue, and organ functional responses. To modulate these responses, other methods have been employed to investigate AQP druggability. This review discusses standard in vitro, in vivo, and in silico methods for studying AQPs, especially for biomedical and mammalian cell biology applications. We also propose some new techniques and approaches for future AQP research to address current gaps in methodology.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"6 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135087095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Getting it right: teaching undergraduate biology to undermine racial essentialism","authors":"Elaine Guevara, Shyamalika Gopalan, Dashiell J Massey, Mayowa Adegboyega, Wen Zhou, Alma Solis, Alisha D Anaya, Steven E Churchill, Joseph Feldblum, Richard Lawler","doi":"10.1093/biomethods/bpad032","DOIUrl":"https://doi.org/10.1093/biomethods/bpad032","url":null,"abstract":"Abstract How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students’ racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students’ racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographic distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students’ endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches instructors can apply when teaching genetics. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"6 9","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135087092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum starvation-based method of ovarian cancer cell dormancy induction and termination in vitro","authors":"Szymon Rutecki, Agnieszka Leśniewska-Bocianowska, Klaudia Chmielewska, Julia Matuszewska, Eryk Naumowicz, Paweł Uruski, Artur Radziemski, Justyna Mikuła-Pietrasik, Andrzej Tykarski, Krzysztof Książek","doi":"10.1093/biomethods/bpad029","DOIUrl":"https://doi.org/10.1093/biomethods/bpad029","url":null,"abstract":"Abstract Awakening and growth reinitiation by dormant cells may contribute to epithelial ovarian cancer (EOC) relapse. The links between these phenomena are loose because of the limited stock of compelling models of EOC dormancy. Here, we show a simple and convenient dormancy research protocol based on serum starvation. This study was conducted on established EOC cell lines A2780, OVCAR-3, and SKOV-3, as well as on primary EOC cells. Cell growth arrest and proliferation were monitored by assessing the Ki67 antigen, PKH26 fluorescence, and cell cycle distribution. In addition, cells were tested for ERK1/2/p38 MAPK activity ratio, apoptosis, and senescence. The study showed that 72-hour serum starvation induces G0/G1 growth arrest of a significant fraction of cells, accompanied by reduced Ki67 and ERK1/2/p38 MAPK activity ratio, without signs of apoptosis or cellular senescence. Moreover, providing cells with 72 hours of a medium enriched in 5% serum allows the culture to regain its proliferative potential. At the same time, we attempted to induce and terminate dormancy with Mitomycin C addition and withdrawal, which were unsuccessful. In conclusion, serum starvation is a convenient way to reliably induce dormancy in EOC cells, allowing them to be efficiently awakened for further mechanistic research in vitro.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"8 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135975794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum Metallomics Reveals Insights into the Associations of Elements with the Progression of Preleukemic Diseases Towards Acute Leukemia","authors":"Amna Jabbar Siddiqui, Noman Khan, Kauser Fatima, Sabiha Farooq, Muhammad Ramzan, Hesham R El-Seedi, Jalal Uddin, Abdullatif Bin Muhsinah, Syed Ghulam Musharraf","doi":"10.1093/biomethods/bpad027","DOIUrl":"https://doi.org/10.1093/biomethods/bpad027","url":null,"abstract":"Abstract Context Acute leukemia (AL) is a critical neoplasm of white blood cells with two main subtypes: acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). Objective This study is focused on understanding the association of the preleukemic disease aplastic anemia (APA) with ALL and AML at metallomic level, using healthy subject as a control. Materials and methods In this study, a validated and efficient ICP-MS/MS-based workflow was employed to profile a total of 13 metallomic features. The study encompassed 41 patients with AML, 62 patients with ALL, 46 patients with APA, and 55 age-matched healthy controls. The metallomic features consisted of 8 essential elements (Ca, Co, Cu, Fe, Mg, Mn, Se, and Zn) and 5 non-essential/toxic elements (Ag, Cd, Cr, Ni, and Pb). Results Six out of the thirteen elements were found to be substantially different (p &amp;lt; 0.05) using absolute concentrations between serum samples of acute leukemia (ALL and AML) and preleukemia (APA) patients in comparison with healthy subjects. Elements including magnesium, calcium, iron, copper and zinc were up-regulated and only one element (chromium) was down-regulated in serum samples of disease when compared with healthy subjects. Discussion Through the utilization of both univariate tests and multivariate classification modeling, it was determined that chromium exhibited a progressive behavior among the studied elements. Specifically, chromium displayed a sequential up-regulation from healthy individuals to preleukemic disease (APA), and ultimately in patients diagnosed with ALL. Conclusion Overall, metallomic-based biomarkers may have utility to predict the association of APA with ALL.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"22 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135455894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency.","authors":"Mario C Chang, Stephen J Staklinski, Matthew E Merritt, Michael S Kilberg","doi":"10.1093/biomethods/bpad026","DOIUrl":"10.1093/biomethods/bpad026","url":null,"abstract":"<p><p>Human asparagine synthetase (ASNS) catalyzes the conversion of aspartate to asparagine in an ATP-dependent reaction that utilizes glutamine as a nitrogen source while generating glutamate, AMP, and pyrophosphate as additional products. Asparagine Synthetase Deficiency (ASNSD) is an inborn error of metabolism in which children present with homozygous or compound heterozygous mutations in the <i>ASNS</i> gene. These mutations result in ASNS variant protein expression. It is believed that these variant ASNS proteins have reduced enzymatic activity or stability resulting in a lack of sufficient asparagine production for cell function. Reduced asparagine production by ASNS appears to severely hinder fetal brain development. Although a variety of approaches for assaying ASNS activity have been reported, we present here a straightforward method for the <i>in vitro</i> enzymatic analysis by detection of AMP production. Our method overcomes limitations in technical feasibility, signal detection, and reproducibility experienced by prior methods like high-performance liquid chromatography, ninhydrin staining, and radioactive tracing. After purification of FLAG-tagged R49Q, G289A, and T337I ASNS variants from stably expressing HEK 293T cells, this method revealed a reduction in activity of 90, 36, and 96%, respectively. Thus, ASNS protein expression and purification, followed by enzymatic activity analysis, has provided a relatively simple protocol to evaluate structure-function relationships for ASNS variants reported for ASNSD patients.</p>","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"8 1","pages":"bpad026"},"PeriodicalIF":3.6,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107592421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of the COVID-19 pandemic on life expectancy in the USA: An application of hybrid life expectancy.","authors":"Warren C Sanderson, Sergei Scherbov","doi":"10.1093/biomethods/bpad025","DOIUrl":"10.1093/biomethods/bpad025","url":null,"abstract":"<p><p>Pandemics are, by definition, temporary intervals of substantially increased mortality rates experienced across a wide geographic area. One way of assessing the magnitude of the COVID-19 pandemic in the USA has been to compute the differences in life expectancy at birth during a pandemic year and the year before the pandemic. Such comparisons are misleading because they do not account for the duration of the pandemic. The computation of life expectancy in 2019 assumes that people spend their entire lives experiencing prepandemic mortality rates. The computation of life expectancy in 2021 assumes that people live their entire lives in a permanent pandemic. However, people do not live their entire lives experiencing the elevated mortality rates of 2021. This article introduces a method for calculating life expectancy that reflects the experience of people enduring pandemic-level mortality rates for fixed durations. We call the new quantity <i>hybrid life expectancy</i> because it integrates both pandemic and prepandemic mortality rates. The difference in life expectancy at birth in the USA in 2019 with and without a 3-year-long pandemic is 0.01 years. This is because mortality rates at ages 0, 1, and 2 in the pandemic were essentially unchanged from their prepandemic levels. Life expectancy at age 65 incorporating a 3-year pandemic is 0.18 years lower than life expectancy would have been without it. Reductions in life expectancy due to the COVID-19 pandemic using hybrid life expectancy are dramatically lower than differences in life expectancy that do not take the duration of the pandemic into account.</p>","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"8 1","pages":"bpad025"},"PeriodicalIF":2.5,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71486944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression.","authors":"Chen Lin, Wei Liu, Wei Jiang, Hongyu Zhao","doi":"10.1093/biomethods/bpad024","DOIUrl":"10.1093/biomethods/bpad024","url":null,"abstract":"<p><p>Genetic association signals have been mostly found in noncoding regions through genome-wide association studies (GWAS), suggesting the roles of gene expression regulation in human diseases and traits. However, there has been limited success in colocalizing expression quantitative trait locus (eQTL) with disease-associated variants. Mediated expression score regression (MESC) is a recently proposed method to quantify the proportion of trait heritability mediated by genetically regulated gene expressions (GReX). Applications of MESC to GWAS results have yielded low estimation of mediated heritability for many traits. As MESC relies on stringent independence assumptions between <i>cis</i>-eQTL effects, gene effects, and nonmediated SNP effects, it may fail to characterize the true relationships between those effect sizes, which leads to biased results. Here, we consider the robustness of MESC to investigate whether the low fraction of mediated heritability inferred by MESC reflects biological reality for complex traits or is an underestimation caused by model misspecifications. Our results suggest that MESC may lead to biased estimates of mediated heritability with misspecification of gene annotations leading to underestimation, whereas misspecification of SNP annotations may lead to overestimation. Furthermore, errors in eQTL effect estimates may lead to underestimation of mediated heritability.</p>","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"8 1","pages":"bpad024"},"PeriodicalIF":3.6,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10599978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71414383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparation and processing of dried blood spots for microRNA sequencing.","authors":"Alice Morgunova, Pascal Ibrahim, Gary Gang Chen, Saché M Coury, Gustavo Turecki, Michael J Meaney, Anthony Gifuni, Ian H Gotlib, Corina Nagy, Tiffany C Ho, Cecilia Flores","doi":"10.1093/biomethods/bpad020","DOIUrl":"10.1093/biomethods/bpad020","url":null,"abstract":"<p><p>Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs (miRNAs)-small non-coding RNAs that regulate gene activity at the post-transcriptional level-are emerging as critical markers and mediators of disease, including cancer, infectious diseases, and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral miRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of miRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of miRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based miRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.</p>","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"8 1","pages":"bpad020"},"PeriodicalIF":3.6,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10603595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71414382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}