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Sampling and analysis methods of air-borne microorganisms in hospital air: a review. 医院空气中气载微生物的采样和分析方法：综述。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2372939
Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu
{"title":"Sampling and analysis methods of air-borne microorganisms in hospital air: a review.","authors":"Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu","doi":"10.1080/07366205.2024.2372939","DOIUrl":"https://doi.org/10.1080/07366205.2024.2372939","url":null,"abstract":"Pathogenic microorganisms can spread in the air as bioaerosols. When the human body is exposed to different bioaerosols, various infectious diseases may occur. As indoor diagnosis and treatment environments, hospitals are relatively closed and have a large flow rate of people. This indoor environment contains complex aerosol components; therefore, effective sampling and detection of microbial elements are essential in airborne pathogen monitoring. This article reviews the sampling and detection of different kinds of microorganisms in bioaerosols from indoor diagnostic and therapeutic settings, with a particular focus on microbial activity. This provides deeper insights into bioaerosols in diagnostic and therapeutic settings.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"9 1","pages":"1-10"},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142177492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system. 有丝分裂的光激活和追逐实验：通过流体交换系统优化通量测量。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-11 DOI: 10.1080/07366205.2024.2372955
Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara
{"title":"Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system.","authors":"Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara","doi":"10.1080/07366205.2024.2372955","DOIUrl":"https://doi.org/10.1080/07366205.2024.2372955","url":null,"abstract":"Modulating autophagy and mitophagy, vital cellular quality control systems, offer therapeutic potential for critical illnesses. However, limited drug screening options hinder progress. We present a novel assay using the photoswitchable fluorescent reporter, mito-Kaede, to quantify mitophagy flux. Mito-Kaede's superior UV-induced photoconversion and brightness post-conversion make it ideal for prolonged mitochondrial dynamics tracking. Its specificity in responding to mitophagy, confirmed by parkin-knockout cells, adds value. When coupled with a custom fluid exchange system, enabling efficient medium changes, precise mitophagy observations become feasible. This mitophagy assay, alongside our methodological insights, can decipher mitophagy's role in pathology and supports drug screening efforts.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"1 1","pages":"1-13"},"PeriodicalIF":2.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142177493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using Longitudinal Variance Components Models to Assess Hyper-connectivity in Severe Traumatic Brain Injury Patients. 利用纵向变异成分模型评估严重脑损伤患者的超连接性。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-07-01 DOI: 10.32598/bcn.2022.3796.1
Keyvan Olazadeh, Nasrin Borumandnia, Mahin Habibi, Hamid Alavi Majd
{"title":"Using Longitudinal Variance Components Models to Assess Hyper-connectivity in Severe Traumatic Brain Injury Patients.","authors":"Keyvan Olazadeh, Nasrin Borumandnia, Mahin Habibi, Hamid Alavi Majd","doi":"10.32598/bcn.2022.3796.1","DOIUrl":"10.32598/bcn.2022.3796.1","url":null,"abstract":"<p><strong>Introduction: </strong>Traumatic brain injury (TBI) is one of the leading causes of death globally and one of the most important diseases indicated by the World Health Organization (WHO). Several studies have concluded that brain damage can dramatically increase functional connectivity (FC) in the brain. The effects of this hyper-connectivity are not yet fully understood and are being studied by neuroscientists. Accordingly, this study identifies areas of the brain where, after brain injury, an acute increase in FC in such areas is observed.</p><p><strong>Methods: </strong>The data used in this study were downloaded from the accessible open functional magnetic resonance imaging (fMRI) site. The data included fMRI of 14 patients with severe TBI and 12 healthy individuals. The longitudinal model of variance components investigated the difference between FC in the baseline effect and the longitudinal trend between the TBI and control groups.</p><p><strong>Results: </strong>After fitting the longitudinal model of variance components, no difference was observed between the FC of the two groups due to the baseline effect. However, in the longitudinal trend of FC, there was a statistically significant difference between the three pairs of cerebellum left, cerebellum right, superior frontal gyrus left, superior frontal gyrus right, thalamus left, and thalamus right in the TBI group compared to the control group.</p><p><strong>Conclusion: </strong>The results showed that FC was sharply increased in 3 pairs of areas in people with TBI. This hyper-connectivity can affect individuals' cognitive functions, including motor and sensory functions. The exact extent of this effect is unclear and requires further investigation by neuroscientists.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"60 1 1","pages":"509-518"},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11565661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90203133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies. Phylobook：从分子系统进化论中显示、注释和提取序列的工具。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-03 DOI: 10.2144/btn-2023-0056
Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner
{"title":"Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies.","authors":"Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner","doi":"10.2144/btn-2023-0056","DOIUrl":"https://doi.org/10.2144/btn-2023-0056","url":null,"abstract":"As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, 'Phylobook' was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. Accurate lineage assignment, which is difficult to automate, is aided using annotations created by different clustering methods. Phylobook provides web-based display combined with automated clustering and manual editing to allow for expert assessment and correction of lineage assignments and extraction for downstream analysis.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"45 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140830012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d. 比较使用 CRISPR-RfxCas13d 在斑马鱼胚胎中进行高通量 RNA 沉默的机器人和人工注射方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2023-0062
Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink
{"title":"Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d.","authors":"Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink","doi":"10.2144/btn-2023-0062","DOIUrl":"10.2144/btn-2023-0062","url":null,"abstract":"<p><p>In this study, the authors compared the efficiency of automated robotic and manual injection methods for the CRISPR-RfxCas13d (CasRx) system for mRNA knockdown and Cas9-mediated DNA targeting in zebrafish embryos. They targeted the no tail (<i>TBXTA</i>) gene as a proof-of-principle, evaluating the induced embryonic phenotypes. Both Cas9 and CasRx systems caused loss of function phenotypes for <i>TBXTA</i>. Cas9 protein exhibited a higher percentage of severe phenotypes compared with mRNA, while CasRx protein and mRNA showed similar efficiency. Both robotic and manual injections demonstrated comparable phenotype percentages and mortality rates. The findings highlight the potential of RNA-targeting CRISPR effectors for precise gene knockdown and endorse automated microinjection at a speed of 1.0 s per embryo as a high-throughput alternative to manual methods.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"183-191"},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples. 比较和优化古代 DNA 样本的方案和全基因组捕获条件。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-03-26 DOI: 10.2144/btn-2023-0107
Reyhan Yaka, Maja Krzewińska, Vendela Kempe Lagerholm, Anna Linderholm, Füsun Özer, Mehmet Somel, Anders Götherström
{"title":"Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.","authors":"Reyhan Yaka, Maja Krzewińska, Vendela Kempe Lagerholm, Anna Linderholm, Füsun Özer, Mehmet Somel, Anders Götherström","doi":"10.2144/btn-2023-0107","DOIUrl":"10.2144/btn-2023-0107","url":null,"abstract":"<p><p>Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"216-223"},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A free and user-friendly software protocol for the quantification of microfauna swimming behavior. 用于量化微型动物游泳行为的免费且用户友好的软件协议。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2024-0001
Colleen M McMaken, Kristin E Gribble
{"title":"A free and user-friendly software protocol for the quantification of microfauna swimming behavior.","authors":"Colleen M McMaken, Kristin E Gribble","doi":"10.2144/btn-2024-0001","DOIUrl":"10.2144/btn-2024-0001","url":null,"abstract":"<p><p>Characterizing swimming behavior can provide a holistic assessment of the health, physiology and ecology of microfaunal species when done in conjunction with measuring other biological parameters. However, tracking and quantifying microfauna swimming behavior using existing automated tools is often difficult due to the animals' small size or transparency, or because of the high cost, expertise, or labor needed for the analysis. To address these issues, we created a cost-effective, user-friendly protocol for behavior analysis that employs the free software packages HitFilm and ToxTrac along with the R package 'trajr' and used the method to quantify the behavior of rotifers. This protocol can be used for other microfaunal species for which investigators may face similar issues in obtaining measurements of swimming behavior.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"174-182"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation and characterization of Paenibacillus peoriae JC-3jx from Dendrobium nobile. 从金钗石斛中分离并鉴定 peoriae JC-3jx Paenibacillus。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-03-12 DOI: 10.2144/btn-2023-0083
ZhiPing Li, Yuan Lin, FeiFei Song, RuoNan Zheng, QinGeng Huang
{"title":"Isolation and characterization of <i>Paenibacillus peoriae</i> JC-3jx from <i>Dendrobium nobile</i>.","authors":"ZhiPing Li, Yuan Lin, FeiFei Song, RuoNan Zheng, QinGeng Huang","doi":"10.2144/btn-2023-0083","DOIUrl":"10.2144/btn-2023-0083","url":null,"abstract":"<p><p><i>Dendrobium</i> is a rich source of high-value natural components. Endophytic fungi are well studied, yet bacteria research is limited. In this study, endophytic bacteria from <i>Dendrobium nobile</i> were isolated using an improved method, showing inhibition of pathogens and growth promotion. JC-3jx, identified as <i>Paenibacillus peoriae</i>, exhibited significant inhibitory activity against tested fungi and bacteria, including <i>Escherichia coli</i>. JC-3jx also promoted corn seed rooting and <i>Dendrobium</i> growth, highlighting its excellent biocontrol and growth-promoting potential.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"192-202"},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140101017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Extraterrestrial agriculture: plant cultivation in space. 地外农业：太空植物栽培。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-11 DOI: 10.2144/btn-2024-0033
Beatrice Bowlby
{"title":"Extraterrestrial agriculture: plant cultivation in space.","authors":"Beatrice Bowlby","doi":"10.2144/btn-2024-0033","DOIUrl":"https://doi.org/10.2144/btn-2024-0033","url":null,"abstract":"[Formula: see text] Researchers are using various techniques and technologies to study how plants grow in extraterrestrial conditions with the hopes of sustaining longer missions for exploring deep space as well as being able to one day cultivate crops on other planets.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"60 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140571236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development and evaluation of a single-tube nested PCR with colorimetric assay for Mycobacterium tuberculosis detection. 开发和评估用于检测结核分枝杆菌的单管巢式 PCR 比色法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-11 DOI: 10.2144/btn-2023-0080
Marcela Pereira Salazar, Juliana Figueiredo da Costa Lima Suassuna Monteiro, Wlisses Henrique Veloso Carvalho-Silva, George Tadeu Nunes Diniz, Roberto Pereira Werkhauser, Lílian Maria Lapa Montenegro, Haiana Charifker Schindler
{"title":"Development and evaluation of a single-tube nested PCR with colorimetric assay for Mycobacterium tuberculosis detection.","authors":"Marcela Pereira Salazar, Juliana Figueiredo da Costa Lima Suassuna Monteiro, Wlisses Henrique Veloso Carvalho-Silva, George Tadeu Nunes Diniz, Roberto Pereira Werkhauser, Lílian Maria Lapa Montenegro, Haiana Charifker Schindler","doi":"10.2144/btn-2023-0080","DOIUrl":"https://doi.org/10.2144/btn-2023-0080","url":null,"abstract":"Molecular techniques have revolutionized tuberculosis (TB) diagnosis by offering a faster and more sensitive approach, detecting <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) DNA directly from samples. Single-tube nested PCR (STNPCR) combines two PCR reactions with separate oligonucleotide sets in a single tube. Moreover, colorimetric methods in PCR products have been studied for pathogen detection. Thus, this study aimed to establish a novel system based on colorimetric STNPCR for <i>Mtb</i> detection using microtiter plates with <i>IS6110</i>-amplified fragments. The results showed a general colorimetric STNPCR detection limit of 1 pg/μl. Its general sensitivity and specificity were 76.62 and 60.53%, respectively, with kappa index agreement of 0.166.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"54 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140603201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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