Alice Baek, Asif Rayhan, Ga-Eun Lee, Sarah Golconda, H. Yu, Shihyoung Kim, P. Limbach, Balasubrahmanyam Addepalli, Sanggu Kim
The biological significance of chemical modifications to the ribonucleic acid (RNA) of human immunodeficiency virus type-1 (HIV-1) has been recognized. However, our understanding of the site-specific and context-dependent roles of these chemical modifications remains limited, primarily due to the absence of nucleotide-resolution mapping of modification sites. In this study, we present a method for achieving nucleotide-resolution mapping of chemical modification sites on HIV-1 RNA using liquid chromatography and tandem mass spectrometry (LC–MS/MS). LC–MS/MS, a powerful tool capable of directly analyzing native RNAs, has proven effective for mapping RNA modifications in small RNA molecules, including ribosomal RNA and transfer RNA. However, longer RNAs have posed challenges, such as the 9 Kb HIV-1 virion RNA, due to the complexity of and ambiguity in mass differences among RNase T1-cleaved RNA fragments in LC-MS/MS data. Here, we introduce a new target RNA enrichment method to isolate small local RNA fragments of HIV-1 RNA that potentially harbor site-specific N6-methyladenosine (m6A) modifications. In our initial trial, we used target-specific DNA probes only and encountered insufficient RNA fragmentation due to inefficient S1 digestion near the target site. Recognizing that inefficient S1 digestion by HIV-1 RNA is likely due to the formation of secondary structures in proximity to the target site, we designed multiple DNA probes annealing to various sites of HIV-1 RNA to better control the structures of RNA substrates for S1 digestion. The use of these non-target DNA probes significantly improved the isolation of more homogeneous target RNA fragments of approximately 50 bases in length. Oligonucleotide LC-MS/MS analysis of these isolated target RNA fragments successfully separated and detected both m6A-methylated and non-methylated oligomers at the two m6A-predicted sites. The principle of this new target enrichment strategy holds promise and should be broadly applicable to the analysis of any lengthy RNA that was previously deemed infeasible for investigation using oligonucleotide LC-MS/MS.
{"title":"Mapping m6A Sites on HIV-1 RNA Using Oligonucleotide LC-MS/MS","authors":"Alice Baek, Asif Rayhan, Ga-Eun Lee, Sarah Golconda, H. Yu, Shihyoung Kim, P. Limbach, Balasubrahmanyam Addepalli, Sanggu Kim","doi":"10.3390/mps7010007","DOIUrl":"https://doi.org/10.3390/mps7010007","url":null,"abstract":"The biological significance of chemical modifications to the ribonucleic acid (RNA) of human immunodeficiency virus type-1 (HIV-1) has been recognized. However, our understanding of the site-specific and context-dependent roles of these chemical modifications remains limited, primarily due to the absence of nucleotide-resolution mapping of modification sites. In this study, we present a method for achieving nucleotide-resolution mapping of chemical modification sites on HIV-1 RNA using liquid chromatography and tandem mass spectrometry (LC–MS/MS). LC–MS/MS, a powerful tool capable of directly analyzing native RNAs, has proven effective for mapping RNA modifications in small RNA molecules, including ribosomal RNA and transfer RNA. However, longer RNAs have posed challenges, such as the 9 Kb HIV-1 virion RNA, due to the complexity of and ambiguity in mass differences among RNase T1-cleaved RNA fragments in LC-MS/MS data. Here, we introduce a new target RNA enrichment method to isolate small local RNA fragments of HIV-1 RNA that potentially harbor site-specific N6-methyladenosine (m6A) modifications. In our initial trial, we used target-specific DNA probes only and encountered insufficient RNA fragmentation due to inefficient S1 digestion near the target site. Recognizing that inefficient S1 digestion by HIV-1 RNA is likely due to the formation of secondary structures in proximity to the target site, we designed multiple DNA probes annealing to various sites of HIV-1 RNA to better control the structures of RNA substrates for S1 digestion. The use of these non-target DNA probes significantly improved the isolation of more homogeneous target RNA fragments of approximately 50 bases in length. Oligonucleotide LC-MS/MS analysis of these isolated target RNA fragments successfully separated and detected both m6A-methylated and non-methylated oligomers at the two m6A-predicted sites. The principle of this new target enrichment strategy holds promise and should be broadly applicable to the analysis of any lengthy RNA that was previously deemed infeasible for investigation using oligonucleotide LC-MS/MS.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439522","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}
Yao Yao, Yibo Zhu, Regina Nogueira, Frank Klawonn, Markus Wallner
Wastewater-based epidemiology (WBE) has great potential to monitor community public health, especially during pandemics. However, it faces substantial hurdles in pathogen surveillance through WBE, encompassing data representativeness, spatiotemporal variability, population estimates, pathogen decay, and environmental factors. This paper aims to enhance the reliability of WBE data, especially for early outbreak detection and improved sampling strategies within sewer networks. The tool implemented in this paper combines a monitoring model and an optimization model to facilitate the optimal selection of sampling points within sewer networks. The monitoring model utilizes parameters such as feces density and average water consumption to define the detectability of the virus that needs to be monitored. This allows for standardization and simplicity in the process of moving from the analysis of wastewater samples to the identification of infection in the source area. The entropy-based model can select optimal sampling points in a sewer network to obtain the most specific information at a minimum cost. The practicality of our tool is validated using data from Hildesheim, Germany, employing SARS-CoV-2 as a pilot pathogen. It is important to note that the tool’s versatility empowers its extension to monitor other pathogens in the future.
{"title":"Optimal Selection of Sampling Points within Sewer Networks for Wastewater-Based Epidemiology Applications","authors":"Yao Yao, Yibo Zhu, Regina Nogueira, Frank Klawonn, Markus Wallner","doi":"10.3390/mps7010006","DOIUrl":"https://doi.org/10.3390/mps7010006","url":null,"abstract":"Wastewater-based epidemiology (WBE) has great potential to monitor community public health, especially during pandemics. However, it faces substantial hurdles in pathogen surveillance through WBE, encompassing data representativeness, spatiotemporal variability, population estimates, pathogen decay, and environmental factors. This paper aims to enhance the reliability of WBE data, especially for early outbreak detection and improved sampling strategies within sewer networks. The tool implemented in this paper combines a monitoring model and an optimization model to facilitate the optimal selection of sampling points within sewer networks. The monitoring model utilizes parameters such as feces density and average water consumption to define the detectability of the virus that needs to be monitored. This allows for standardization and simplicity in the process of moving from the analysis of wastewater samples to the identification of infection in the source area. The entropy-based model can select optimal sampling points in a sewer network to obtain the most specific information at a minimum cost. The practicality of our tool is validated using data from Hildesheim, Germany, employing SARS-CoV-2 as a pilot pathogen. It is important to note that the tool’s versatility empowers its extension to monitor other pathogens in the future.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139383979","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}
J. L. Aeberhard, A. Radan, Ramin Abolfazl Soltani, K. Strahm, S. Schneider, Adriana Carrié, Mathieu Lemay, Jens Krauss, Ricard Delgado-Gonzalo, Daniel Surbek
Artificial intelligence (AI) is gaining increasing interest in the field of medicine because of its capacity to process big data and pattern recognition. Cardiotocography (CTG) is widely used for the assessment of foetal well-being and uterine contractions during pregnancy and labour. It is characterised by inter- and intraobserver variability in interpretation, which depends on the observers’ experience. Artificial intelligence (AI)-assisted interpretation could improve its quality and, thus, intrapartal care. Cardiotocography (CTG) raw signals from labouring women were extracted from the database at the University Hospital of Bern between 2006 and 2019. Later, they were matched with the corresponding foetal outcomes, namely arterial umbilical cord pH and 5-min APGAR score. Excluded were deliveries where data were incomplete, as well as multiple births. Clinical data were grouped regarding foetal pH and APGAR score at 5 min after delivery. Physiological foetal pH was defined as 7.15 and above, and a 5-min APGAR score was considered physiologic when reaching ≥7. With these groups, the algorithm was trained to predict foetal hypoxia. Raw data from 19,399 CTG recordings could be exported. This was accomplished by manually searching the patient’s identification numbers (PIDs) and extracting the corresponding raw data from each episode. For some patients, only one episode per pregnancy could be found, whereas for others, up to ten episodes were available. Initially, 3400 corresponding clinical outcomes were found for the 19,399 CTGs (17.52%). Due to the small size, this dataset was rejected, and a new search strategy was elaborated. After further matching and curation, 6141 (31.65%) paired data samples could be extracted (cardiotocography raw data and corresponding maternal and foetal outcomes). Of these, half will be used to train artificial intelligence (AI) algorithms, whereas the other half will be used for analysis of efficacy. Complete data could only be found for one-third of the available population. Yet, to our knowledge, this is the most exhaustive and second-largest cardiotocography database worldwide, which can be used for computer analysis and programming. A further enrichment of the database is planned.
{"title":"Introducing Artificial Intelligence in Interpretation of Foetal Cardiotocography: Medical Dataset Curation and Preliminary Coding—An Interdisciplinary Project","authors":"J. L. Aeberhard, A. Radan, Ramin Abolfazl Soltani, K. Strahm, S. Schneider, Adriana Carrié, Mathieu Lemay, Jens Krauss, Ricard Delgado-Gonzalo, Daniel Surbek","doi":"10.3390/mps7010005","DOIUrl":"https://doi.org/10.3390/mps7010005","url":null,"abstract":"Artificial intelligence (AI) is gaining increasing interest in the field of medicine because of its capacity to process big data and pattern recognition. Cardiotocography (CTG) is widely used for the assessment of foetal well-being and uterine contractions during pregnancy and labour. It is characterised by inter- and intraobserver variability in interpretation, which depends on the observers’ experience. Artificial intelligence (AI)-assisted interpretation could improve its quality and, thus, intrapartal care. Cardiotocography (CTG) raw signals from labouring women were extracted from the database at the University Hospital of Bern between 2006 and 2019. Later, they were matched with the corresponding foetal outcomes, namely arterial umbilical cord pH and 5-min APGAR score. Excluded were deliveries where data were incomplete, as well as multiple births. Clinical data were grouped regarding foetal pH and APGAR score at 5 min after delivery. Physiological foetal pH was defined as 7.15 and above, and a 5-min APGAR score was considered physiologic when reaching ≥7. With these groups, the algorithm was trained to predict foetal hypoxia. Raw data from 19,399 CTG recordings could be exported. This was accomplished by manually searching the patient’s identification numbers (PIDs) and extracting the corresponding raw data from each episode. For some patients, only one episode per pregnancy could be found, whereas for others, up to ten episodes were available. Initially, 3400 corresponding clinical outcomes were found for the 19,399 CTGs (17.52%). Due to the small size, this dataset was rejected, and a new search strategy was elaborated. After further matching and curation, 6141 (31.65%) paired data samples could be extracted (cardiotocography raw data and corresponding maternal and foetal outcomes). Of these, half will be used to train artificial intelligence (AI) algorithms, whereas the other half will be used for analysis of efficacy. Complete data could only be found for one-third of the available population. Yet, to our knowledge, this is the most exhaustive and second-largest cardiotocography database worldwide, which can be used for computer analysis and programming. A further enrichment of the database is planned.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139385685","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}
Introduction: Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) remain major public health issues in sub-Saharan Africa. The co-occurrence of these diseases is a growing concern in the region, and social determinants, the circumstances under which people are born, live, work, and age, are known to influence the risk of disease transmission, diagnosis, treatment, and outcomes. Here, we present a protocol for the evidence synthesis on the social determinants of HIV/TB coinfections in sub-Saharan Africa. The high prevalence of Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) in sub-Saharan Africa presents significant public health challenges. TB/HIV comorbidity is influenced by various social determinants, including social, economic, cultural, and environmental factors, impacting disease transmission risk, accurate diagnosis, and treatment outcomes. This study protocol aims to provide an evidence synthesis on the social determinants of HIV/TB coinfection in sub-Saharan Africa. Methods and analysis: The researchers will use the Arksey and O’Malley’s (2005) methodological framework to guide the scoping review. First, databases such as PubMed, MEDLINE, Web of Science, and PsychInfo will be searched. The researchers will then proceed in two steps. Before finalising the study selection, two independent reviewers will examine the article titles and abstracts for eligibility and inclusion. The researchers will then conduct a full-text screening of the articles based on the selected titles and abstracts. The authors’ tool will be used to extract data, ensuring that the articles are properly screened and that the risk of bias is minimized. The chosen studies will be examined using a standardized tool to examine all bibliographic data and study characteristics. Ethics and dissemination: The review will provide an overview of the social determinants influencing the prevalence and outcomes of TB/HIV comorbidity in the region, as well as identify any research gaps. Policymakers, researchers, and healthcare professionals will benefit from the findings in developing targeted interventions to address the social determinants of TB/HIV comorbidity in sub-Saharan Africa.
{"title":"A Scoping Review Protocol of Social Determinants of HIV/TB Coinfections in Sub-Saharan Africa","authors":"Lucas Banda, Olanrewaju Oladimeji","doi":"10.3390/mps7010004","DOIUrl":"https://doi.org/10.3390/mps7010004","url":null,"abstract":"Introduction: Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) remain major public health issues in sub-Saharan Africa. The co-occurrence of these diseases is a growing concern in the region, and social determinants, the circumstances under which people are born, live, work, and age, are known to influence the risk of disease transmission, diagnosis, treatment, and outcomes. Here, we present a protocol for the evidence synthesis on the social determinants of HIV/TB coinfections in sub-Saharan Africa. The high prevalence of Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) in sub-Saharan Africa presents significant public health challenges. TB/HIV comorbidity is influenced by various social determinants, including social, economic, cultural, and environmental factors, impacting disease transmission risk, accurate diagnosis, and treatment outcomes. This study protocol aims to provide an evidence synthesis on the social determinants of HIV/TB coinfection in sub-Saharan Africa. Methods and analysis: The researchers will use the Arksey and O’Malley’s (2005) methodological framework to guide the scoping review. First, databases such as PubMed, MEDLINE, Web of Science, and PsychInfo will be searched. The researchers will then proceed in two steps. Before finalising the study selection, two independent reviewers will examine the article titles and abstracts for eligibility and inclusion. The researchers will then conduct a full-text screening of the articles based on the selected titles and abstracts. The authors’ tool will be used to extract data, ensuring that the articles are properly screened and that the risk of bias is minimized. The chosen studies will be examined using a standardized tool to examine all bibliographic data and study characteristics. Ethics and dissemination: The review will provide an overview of the social determinants influencing the prevalence and outcomes of TB/HIV comorbidity in the region, as well as identify any research gaps. Policymakers, researchers, and healthcare professionals will benefit from the findings in developing targeted interventions to address the social determinants of TB/HIV comorbidity in sub-Saharan Africa.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139385505","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}
Hai Dang Ngo, Jan Patrick Formanski, Vivien Grunwald, Birco Schwalbe, Michael Schreiber
Flaviviruses are a family of RNA viruses that includes many known pathogens, such as Zika virus (ZIKV), West Nile virus (WNV), dengue virus (DENV), and yellow fever virus (YFV). A pseudotype is an artificial virus particle created in vitro by incorporating the flavivirus envelope proteins into the structure of, for example, a retrovirus such as human immunodeficiency virus type-1 (HIV-1). They can be a useful tool in virology for understanding the biology of flaviviruses, evaluating immune responses, developing antiviral strategies but can also be used as vectors for gene transfer experiments. This protocol describes the generation of a ZIKV/HIV-1 pseudotype developed as a new tool for infecting cells derived from a highly malignant brain tumor: glioblastoma multiforme grade 4.
{"title":"Generation of Viral Particles with Brain Cell-Specific Tropism by Pseudotyping HIV-1 with the Zika Virus E Protein","authors":"Hai Dang Ngo, Jan Patrick Formanski, Vivien Grunwald, Birco Schwalbe, Michael Schreiber","doi":"10.3390/mps7010003","DOIUrl":"https://doi.org/10.3390/mps7010003","url":null,"abstract":"Flaviviruses are a family of RNA viruses that includes many known pathogens, such as Zika virus (ZIKV), West Nile virus (WNV), dengue virus (DENV), and yellow fever virus (YFV). A pseudotype is an artificial virus particle created in vitro by incorporating the flavivirus envelope proteins into the structure of, for example, a retrovirus such as human immunodeficiency virus type-1 (HIV-1). They can be a useful tool in virology for understanding the biology of flaviviruses, evaluating immune responses, developing antiviral strategies but can also be used as vectors for gene transfer experiments. This protocol describes the generation of a ZIKV/HIV-1 pseudotype developed as a new tool for infecting cells derived from a highly malignant brain tumor: glioblastoma multiforme grade 4.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139150253","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}
Inês M Ferreira, Luz Murillo, Jean-Marie Le-Corre, Marco Correia, Rita Anastácio, Mário J Pereira
The scarcity on the Atlantic coast of the African sea turtle population and its dynamics data is well known. This article discusses the nesting ecology methods and analysis of a nascent Angolan project aimed at preserving the nesting female population of the Olive Ridley turtle (Lepidochelys olivacea) on the coast of Lobito. This study examines the nesting ecology of this species from 2020 to 2023. Females had an average CCL of 70.2 cm and CCW of 68.5 cm. These females laid 127 eggs in nests that averaged 47.0 cm deep. The ex situ nest incubation period averaged 60 days, and the hatchling success was 82.1%. Some techniques used in this project require modifications and enhancements. The utilization of photo identification did not yield the anticipated outcomes, prompting the adoption of passive integrated transponders (PITs) in the last season. However, due to limited funding, the success of this method is contingent upon an augmented field effort, allowing for the recapture of a larger number of females. The continuity of this project hinges upon collaboration between higher authorities and the local community. Together, it is possible to deepen the understanding of the nesting ecology of this species and address pivotal issues for its conservation, thereby implementing the most effective preservation measures.
{"title":"Nesting Ecology of <i>Lepidochelys olivacea</i> in Lobito, Angola.","authors":"Inês M Ferreira, Luz Murillo, Jean-Marie Le-Corre, Marco Correia, Rita Anastácio, Mário J Pereira","doi":"10.3390/mps7010002","DOIUrl":"10.3390/mps7010002","url":null,"abstract":"<p><p>The scarcity on the Atlantic coast of the African sea turtle population and its dynamics data is well known. This article discusses the nesting ecology methods and analysis of a nascent Angolan project aimed at preserving the nesting female population of the Olive Ridley turtle (<i>Lepidochelys olivacea</i>) on the coast of Lobito. This study examines the nesting ecology of this species from 2020 to 2023. Females had an average CCL of 70.2 cm and CCW of 68.5 cm. These females laid 127 eggs in nests that averaged 47.0 cm deep. The <i>ex situ</i> nest incubation period averaged 60 days, and the hatchling success was 82.1%. Some techniques used in this project require modifications and enhancements. The utilization of photo identification did not yield the anticipated outcomes, prompting the adoption of passive integrated transponders (PITs) in the last season. However, due to limited funding, the success of this method is contingent upon an augmented field effort, allowing for the recapture of a larger number of females. The continuity of this project hinges upon collaboration between higher authorities and the local community. Together, it is possible to deepen the understanding of the nesting ecology of this species and address pivotal issues for its conservation, thereby implementing the most effective preservation measures.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10801490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512993","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}
Jong H. Kim, K. Chan, W. Hart-Cooper, DeAngela Ford, Kaydren Orcutt, Jeffrey D Palumbo, Christina C. Tam, William J. Orts
The United States is a principal producer of tree nuts (almonds, pistachios, and walnuts), resulting in the generation of excess of tree-nutshell by-products each year, with few market outlets. A nutshell is an essential, lignocellulosic layer that protects a kernel (seed) from the environment during cultivation. The objective of this study was to develop nutshell by-products as herbicide delivery systems, which would not only enable sustainable weed control in fields but also increases nutshell value and reduce the cost of waste disposal. We recently identified a natural salicylaldehyde (SA) that emits volatiles with both herbicidal and antifungal properties. In this study, walnut shell particles saturated with 0.8 to 1.6 M SA were developed as delivery vehicles for SA to soil, which allowed for the controlled release of an SA fumigant for weed control. The pre- and post-emergent herbicidal efficacy of SA was investigated using model monocot (Lolium arundinaceum (Schreb.) Darbysh; turfgrass) and dicot (Brassica rapa var. pekinensis; Chinese cabbage) plants. We compared (1) the effects of different types of solvents for dissolving SA (dimethyl sulfoxide (DMSO) and ethanol (60%, v/v)), and (2) the effect of covering soil with plastic layers (i.e., soil pasteurization) or not covering soil during SA fumigation using nutshells. Results: In the pre-emergent herbicidal testing with the soil covered, the dicot plants exhibited levels of higher susceptibility to SA in DMSO emitted from nutshells when compared to the monocot plants. The seed germination frequencies in the dicots were 15% and 1% with 0.8 and 1.6 M SA, respectively, while those in the monocots were 32% and 18%, respectively, under the same test conditions. In the post-emergent herbicidal testing with the soil covered, the growth of both the monocot and dicot plants was completely prevented after 5 to 7 days of SA fumigation, resulting in the deaths of entire plants. It was noteworthy that in the post-emergent herbicidal testing, SA dissolved in ethanol (60%, v/v) completely disrupted the growth of the monocot and dicot plants as early as 3 days after SA emission from the nutshells, even without the soil being covered. Tree-nutshell particles could serve as effective SA delivery vehicles with controlled release capabilities for SA. The SA exhibited pre- and post-emergent herbicidal activities against the monocot and dicot plants at most growth stages. SA (0.8 and 1.6 M) dissolved in ethanol (60%, v/v) might exert a synergism for higher herbicidal activity after emission from nutshells. Since tree nuts capture/store a substantial amount of carbon over their life-cycles, the new and sustainable utility of using nutshells not only reduces carbon emissions but also valorizes tree-nut by-products, thus benefitting the tree-nut industry.
美国是树坚果（杏仁、开心果和核桃）的主要生产国，因此每年都会产生过量的树坚果壳副产品，但市场销路却很少。坚果壳是一种重要的木质纤维素层，可在种植过程中保护果仁（种子）免受环境影响。本研究的目的是开发果壳副产品作为除草剂的输送系统，这不仅能实现田间除草的可持续性，还能提高果壳的价值并降低废物处理成本。我们最近发现了一种天然水杨醛（SA），它能释放出具有除草和抗真菌特性的挥发性物质。在这项研究中，我们开发了饱和 0.8 至 1.6 M 水杨醛的核桃壳颗粒，作为水杨醛在土壤中的输送载体，从而控制水杨醛熏蒸剂的释放以控制杂草。我们使用示范单子叶植物（Lolium arundinaceum (Schreb.) Darbysh；草皮草）和双子叶植物（Brassica rapa var.我们比较了（1）不同类型溶剂（二甲基亚砜（DMSO）和乙醇（60%，v/v））溶解 SA 的效果，以及（2）在使用果壳熏蒸 SA 的过程中用塑料层覆盖土壤（即土壤杀菌）或不覆盖土壤的效果。研究结果在覆盖土壤的萌发前除草试验中，与单子叶植物相比，双子叶植物对果壳释放的二甲基亚砜中的 SA 表现出更高的敏感性。在相同的试验条件下，双子叶植物的种子萌发率在 0.8 和 1.6 M SA 的作用下分别为 15%和 1%，而单子叶植物的种子萌发率分别为 32% 和 18%。在覆盖土壤的苗后除草试验中，单子叶植物和双子叶植物在 SA 熏蒸 5 至 7 天后生长完全受阻，导致整株植物死亡。值得注意的是，在芽后除草试验中，溶解在乙醇（60%，v/v）中的 SA 在果壳释放出 SA 后 3 天就完全破坏了单子叶植物和双子叶植物的生长，即使没有覆盖土壤也是如此。果壳颗粒可作为有效的 SA 运送载体，具有控制 SA 释放的能力。在大多数生长阶段，SA 对单子叶植物和双子叶植物都具有萌芽前和萌芽后除草活性。溶解在乙醇（60%，v/v）中的 SA（0.8 和 1.6 M）从果壳中释放出来后，可能会产生增效作用，从而提高除草活性。由于树坚果在其生命周期中会捕获/储存大量的碳，因此利用坚果壳这种可持续的新方法不仅能减少碳排放，还能使树坚果副产品增值，从而使树坚果产业受益。
{"title":"Valorizing Tree-Nutshell Particles as Delivery Vehicles for a Natural Herbicide","authors":"Jong H. Kim, K. Chan, W. Hart-Cooper, DeAngela Ford, Kaydren Orcutt, Jeffrey D Palumbo, Christina C. Tam, William J. Orts","doi":"10.3390/mps7010001","DOIUrl":"https://doi.org/10.3390/mps7010001","url":null,"abstract":"The United States is a principal producer of tree nuts (almonds, pistachios, and walnuts), resulting in the generation of excess of tree-nutshell by-products each year, with few market outlets. A nutshell is an essential, lignocellulosic layer that protects a kernel (seed) from the environment during cultivation. The objective of this study was to develop nutshell by-products as herbicide delivery systems, which would not only enable sustainable weed control in fields but also increases nutshell value and reduce the cost of waste disposal. We recently identified a natural salicylaldehyde (SA) that emits volatiles with both herbicidal and antifungal properties. In this study, walnut shell particles saturated with 0.8 to 1.6 M SA were developed as delivery vehicles for SA to soil, which allowed for the controlled release of an SA fumigant for weed control. The pre- and post-emergent herbicidal efficacy of SA was investigated using model monocot (Lolium arundinaceum (Schreb.) Darbysh; turfgrass) and dicot (Brassica rapa var. pekinensis; Chinese cabbage) plants. We compared (1) the effects of different types of solvents for dissolving SA (dimethyl sulfoxide (DMSO) and ethanol (60%, v/v)), and (2) the effect of covering soil with plastic layers (i.e., soil pasteurization) or not covering soil during SA fumigation using nutshells. Results: In the pre-emergent herbicidal testing with the soil covered, the dicot plants exhibited levels of higher susceptibility to SA in DMSO emitted from nutshells when compared to the monocot plants. The seed germination frequencies in the dicots were 15% and 1% with 0.8 and 1.6 M SA, respectively, while those in the monocots were 32% and 18%, respectively, under the same test conditions. In the post-emergent herbicidal testing with the soil covered, the growth of both the monocot and dicot plants was completely prevented after 5 to 7 days of SA fumigation, resulting in the deaths of entire plants. It was noteworthy that in the post-emergent herbicidal testing, SA dissolved in ethanol (60%, v/v) completely disrupted the growth of the monocot and dicot plants as early as 3 days after SA emission from the nutshells, even without the soil being covered. Tree-nutshell particles could serve as effective SA delivery vehicles with controlled release capabilities for SA. The SA exhibited pre- and post-emergent herbicidal activities against the monocot and dicot plants at most growth stages. SA (0.8 and 1.6 M) dissolved in ethanol (60%, v/v) might exert a synergism for higher herbicidal activity after emission from nutshells. Since tree nuts capture/store a substantial amount of carbon over their life-cycles, the new and sustainable utility of using nutshells not only reduces carbon emissions but also valorizes tree-nut by-products, thus benefitting the tree-nut industry.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139170554","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}
Johanna Alm, Benoit Fischer, Alexandra Emanuela Burger, Francesca Moretti
Perturbation of angiogenesis is associated with a variety of diseases and pro- as well as antiangiogenic therapies are being actively explored. Additionally, unintended adverse drug effects on angiogenesis might lead to promotion of tumor progression and cardiovascular complications. Several tri-dimensional microfluidic vessel-on-chip systems have been described that allow a more accurate investigation of vascular physiology and pathology, compared to the two-dimensional static culture of endothelial cells. The OrganoPlate® angiogenesis-on-chip system has been demonstrated to be amenable to high-throughput screening for the antiangiogenic properties of molecules. We set out to adapt this system for high-throughput screening of molecules with proangiogenic properties. Our technical advancement of the OrganoPlate® angiogenesis-on-chip assay expands its applicability in the early screening of both anti- as well as proangiogenic properties of compounds for therapeutic modulation of angiogenesis as well as the identification of angiogenesis-associated drug-induced vascular toxicities.
{"title":"Development of a 3D Perfused In Vitro System to Assess Proangiogenic Properties of Compounds.","authors":"Johanna Alm, Benoit Fischer, Alexandra Emanuela Burger, Francesca Moretti","doi":"10.3390/mps6060119","DOIUrl":"10.3390/mps6060119","url":null,"abstract":"<p><p>Perturbation of angiogenesis is associated with a variety of diseases and pro- as well as antiangiogenic therapies are being actively explored. Additionally, unintended adverse drug effects on angiogenesis might lead to promotion of tumor progression and cardiovascular complications. Several tri-dimensional microfluidic vessel-on-chip systems have been described that allow a more accurate investigation of vascular physiology and pathology, compared to the two-dimensional static culture of endothelial cells. The OrganoPlate<sup>®</sup> angiogenesis-on-chip system has been demonstrated to be amenable to high-throughput screening for the antiangiogenic properties of molecules. We set out to adapt this system for high-throughput screening of molecules with proangiogenic properties. Our technical advancement of the OrganoPlate<sup>®</sup> angiogenesis-on-chip assay expands its applicability in the early screening of both anti- as well as proangiogenic properties of compounds for therapeutic modulation of angiogenesis as well as the identification of angiogenesis-associated drug-induced vascular toxicities.</p>","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10745376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138830498","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}
Junchi Huang, Mikael Montelius, Jan-Erik Damber, K. Welén
Bone metastases cause morbidity and mortality in several human cancer forms. Experimental models are used to unravel the mechanisms and identify possible treatment targets. The location inside the skeleton complicates accurate assessment. This study evaluates the performance of magnetic resonance imaging (MRI) of prostate cancer tumors growing intratibially in mice. MRI detected intratibial tumor lesions with a sensitivity and specificity of 100% and 89%, respectively, compared to histological evaluation. Location and some phenotypical features could also be readily detected with MRI. Regarding volume estimation, the correlation between MRI and histological assessment was high (p < 0.001, r = 0.936). In conclusion, this study finds MRI to be a reliable tool for in vivo, non-invasive, non-ionizing, real-time monitoring of intratibial tumor growth.
骨转移在几种人类癌症中引起发病率和死亡率。实验模型用于揭示机制和确定可能的治疗靶点。骨骼内部的位置使准确评估变得复杂。本研究评价了磁共振成像(MRI)对小鼠腹腔内生长的前列腺癌肿瘤的表现。与组织学评估相比，MRI检测胫骨内肿瘤病变的敏感性和特异性分别为100%和89%。位置和一些表型特征也可以很容易地通过MRI检测到。在体积估计方面，MRI与组织学评估的相关性较高(p < 0.001, r = 0.936)。总之，本研究发现MRI是一种可靠的工具，可以在体内、无创、非电离、实时监测胫骨内肿瘤的生长。
{"title":"Magnetic Resonance Imaging as a Tool for Monitoring Intratibial Growth of Experimental Prostate Cancer Metastases in Mice","authors":"Junchi Huang, Mikael Montelius, Jan-Erik Damber, K. Welén","doi":"10.3390/mps6060118","DOIUrl":"https://doi.org/10.3390/mps6060118","url":null,"abstract":"Bone metastases cause morbidity and mortality in several human cancer forms. Experimental models are used to unravel the mechanisms and identify possible treatment targets. The location inside the skeleton complicates accurate assessment. This study evaluates the performance of magnetic resonance imaging (MRI) of prostate cancer tumors growing intratibially in mice. MRI detected intratibial tumor lesions with a sensitivity and specificity of 100% and 89%, respectively, compared to histological evaluation. Location and some phenotypical features could also be readily detected with MRI. Regarding volume estimation, the correlation between MRI and histological assessment was high (p < 0.001, r = 0.936). In conclusion, this study finds MRI to be a reliable tool for in vivo, non-invasive, non-ionizing, real-time monitoring of intratibial tumor growth.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138598703","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}
A. van Duinkerken, M. Bosmans, C. Baliatsas, N. Tak, A. Meerdink, N. Jansen, M. de Vetten-Mc Mahon, E. Marra, M. Dückers
Background: The global COVID-19 pandemic has profoundly affected public health. Directly, the pandemic resulted in over 6.6 million deaths, numerous hospitalizations, and widespread illness. The pandemic has also affected health indirectly through government-imposed protective measures, causing decline in mental well-being and increasing social isolation. Unlike previous disasters or crises, the pandemic’s worldwide and enduring impact necessitates a unique research approach. The Network for Health Research in Disasters in the Netherlands responded by initiating a longitudinal, extensive research project called the Integrated Health Monitor COVID-19. The Integrated Health Monitor COVID-19 explores both the direct and indirect health effects of the pandemic at the population level. Methods: The Integrated Health Monitor COVID-19 employs a dual-pronged monitoring strategy alongside an annual literature review. This strategy comprises short-cycle monitoring (conducted quarterly) and long-cycle monitoring (conducted once every one or two years). This comprehensive approach enables the evaluation of health trends during the pandemic, facilitating comparisons with pre-pandemic levels and identification of risk and protective factors. Both monitoring methods incorporate data from surveys and general practice registries. The integration of annual literature reviews with these measurements enables iterative research, while dialogues on policy and practice improvements enhance the knowledge-to-action process. Discussion: Much of the existing knowledge about the potential impact of the COVID-19 pandemic is derived from research on sudden-onset disasters limited to specific geographical areas. This study is anticipated to provide valuable fresh insights into the evolving dynamics of population health and specific vulnerabilities within the ongoing pandemic context.
{"title":"The Integrated Health Monitor COVID-19: A Protocol for a Comprehensive Assessment of the Short- and Long-Term Health Impact of the Pandemic in the Netherlands","authors":"A. van Duinkerken, M. Bosmans, C. Baliatsas, N. Tak, A. Meerdink, N. Jansen, M. de Vetten-Mc Mahon, E. Marra, M. Dückers","doi":"10.3390/mps6060117","DOIUrl":"https://doi.org/10.3390/mps6060117","url":null,"abstract":"Background: The global COVID-19 pandemic has profoundly affected public health. Directly, the pandemic resulted in over 6.6 million deaths, numerous hospitalizations, and widespread illness. The pandemic has also affected health indirectly through government-imposed protective measures, causing decline in mental well-being and increasing social isolation. Unlike previous disasters or crises, the pandemic’s worldwide and enduring impact necessitates a unique research approach. The Network for Health Research in Disasters in the Netherlands responded by initiating a longitudinal, extensive research project called the Integrated Health Monitor COVID-19. The Integrated Health Monitor COVID-19 explores both the direct and indirect health effects of the pandemic at the population level. Methods: The Integrated Health Monitor COVID-19 employs a dual-pronged monitoring strategy alongside an annual literature review. This strategy comprises short-cycle monitoring (conducted quarterly) and long-cycle monitoring (conducted once every one or two years). This comprehensive approach enables the evaluation of health trends during the pandemic, facilitating comparisons with pre-pandemic levels and identification of risk and protective factors. Both monitoring methods incorporate data from surveys and general practice registries. The integration of annual literature reviews with these measurements enables iterative research, while dialogues on policy and practice improvements enhance the knowledge-to-action process. Discussion: Much of the existing knowledge about the potential impact of the COVID-19 pandemic is derived from research on sudden-onset disasters limited to specific geographical areas. This study is anticipated to provide valuable fresh insights into the evolving dynamics of population health and specific vulnerabilities within the ongoing pandemic context.","PeriodicalId":18715,"journal":{"name":"Methods and Protocols","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138607327","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}
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