Essays in biochemistry最新文献_第5页

Computational methods for processing and interpreting mass spectrometry-based metabolomics. 处理和解释基于质谱的代谢组学的计算方法。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-04-30 DOI: 10.1042/EBC20230019

Leonardo Perez de Souza, Alisdair R Fernie

{"title":"Computational methods for processing and interpreting mass spectrometry-based metabolomics.","authors":"Leonardo Perez de Souza, Alisdair R Fernie","doi":"10.1042/EBC20230019","DOIUrl":"10.1042/EBC20230019","url":null,"abstract":"Metabolomics has emerged as an indispensable tool for exploring complex biological questions, providing the ability to investigate a substantial portion of the metabolome. However, the vast complexity and structural diversity intrinsic to metabolites imposes a great challenge for data analysis and interpretation. Liquid chromatography mass spectrometry (LC-MS) stands out as a versatile technique offering extensive metabolite coverage. In this mini-review, we address some of the hurdles posed by the complex nature of LC-MS data, providing a brief overview of computational tools designed to help tackling these challenges. Our focus centers on two major steps that are essential to most metabolomics investigations: the translation of raw data into quantifiable features, and the extraction of structural insights from mass spectra to facilitate metabolite identification. By exploring current computational solutions, we aim at providing a critical overview of the capabilities and constraints of mass spectrometry-based metabolomics, while introduce some of the most recent trends in data processing and analysis within the field.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"5-13"},"PeriodicalIF":6.4,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138298743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Kinetic modelling of glycolytic oscillations. 糖酵解振荡的动力学模型。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-04-30 DOI: 10.1042/EBC20230037

David D van Niekerk, Morne van Wyk, Theresa Kouril, Jacky L Snoep

引用次数: 0

Oxysterol sulfates in fluids, cells and tissues: how much do we know about their clinical significance, biological relevance and biophysical implications? 体液、细胞和组织中的氧基甾醇硫酸盐：我们对其临床意义、生物学相关性和生物物理影响了解多少？

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-03-28 DOI: 10.1042/EBC20230090

Ana Reis, Irundika H K Dias

{"title":"Oxysterol sulfates in fluids, cells and tissues: how much do we know about their clinical significance, biological relevance and biophysical implications?","authors":"Ana Reis, Irundika H K Dias","doi":"10.1042/EBC20230090","DOIUrl":"https://doi.org/10.1042/EBC20230090","url":null,"abstract":"Oxysterol sulfates are emerging as key players in lipid homeostasis, inflammation and immunity. Despite this, knowledge on their basal levels in fluids, cells and tissues and any changes associated with age, gender and diet in health and disease; as well as their spatio-temporal distribution in cell membranes and organelles have been greatly hampered by the lack of commercially available pure synthetic standards. Expansion of the panel of pure oxysterol sulfates standards is pivotal to improve our understanding on the impact of oxysterol sulfates at the membrane level and their role in cellular events. While the clinical significance, biophysical implications and biological relevance of oxysterol sulfates in fluids, cells and tissues remains largely unknown, knowledge already gathered on the precursors of oxysterol sulfates (e.g. oxysterols and cholesterol sulfate) can be used to guide researchers on the most relevant aspects to search for when screening for oxysterol sulfates bioavailability in (patho)physiological conditions which are crucial in the design of biophysical and of cell-based assays. Herein, we provide a review on the brief knowledge involving oxysterol sulfate and an overview on the biophysical implications and biological relevance of oxysterols and cholesterol sulfate useful to redirect further investigations on the role of oxysterol sulfates in health and disease.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rapid Superficial Vein Assessment (RaSuVA): A pre-procedural systematic evaluation of superficial veins to optimize venous catheterization in neonates. 浅静脉快速评估 (RaSuVA)：对浅静脉进行术前系统评估，以优化新生儿静脉导管插入术。

2区生物学

Essays in biochemistry Pub Date : 2024-01-01 Epub Date: 2022-05-20 DOI: 10.1177/11297298221098481

Vito D'Andrea, Giorgia Prontera, Lucilla Pezza, Giovanni Barone, Giovanni Vento, Mauro Pittiruti

{"title":"Rapid Superficial Vein Assessment (RaSuVA): A pre-procedural systematic evaluation of superficial veins to optimize venous catheterization in neonates.","authors":"Vito D'Andrea, Giorgia Prontera, Lucilla Pezza, Giovanni Barone, Giovanni Vento, Mauro Pittiruti","doi":"10.1177/11297298221098481","DOIUrl":"10.1177/11297298221098481","url":null,"abstract":"Background: Placement of peripheral intra-venous cannulas and epicutaneo-caval catheters is routinely performed in in Neonatal Intensive Care Unit (NICU), and both devices require visible superficial veins easy to cannulate. NICU patients are intrinsically characterized by poor and fragile vein asset, so that puncture and cannulation of superficial veins is often a challenge even for trained clinicians and cannulation frequently results in a stressful, painful, difficult procedure.Methods and results: Rapid Superficial Vein Assessment is meant to offer a systematic pre-procedural evaluation of all superficial veins of the newborn, so to allow a rational choice of the best insertion site, tailored on the single patient, and optimized for the specific type of venous access device. The superficial veins are examined systematically, both with and without NIR technology, exploring seven skin areas in the following order: (1) medial malleolus, (2) lateral malleolus, (3) retro-popliteal fossa, (4) back of the hand and wrist, (5) antecubital fossa, (6) anterior scalp surface, and (7) posterior scalp surface.Conclusions: The aim of the protocol is to increase the first attempt success rate and reduce the duration of the procedure, the number of attempts for single patient and possibly to limit complications, stress, and pain in neonates.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"63 1","pages":"303-307"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89625010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Understanding biochemistry: basic aspects of statistics for life sciences. 理解生物化学:生命科学统计的基本方面。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-10-25 DOI: 10.1042/EBC20220211

Donald Reid

{"title":"Understanding biochemistry: basic aspects of statistics for life sciences.","authors":"Donald Reid","doi":"10.1042/EBC20220211","DOIUrl":"10.1042/EBC20220211","url":null,"abstract":"If the biological world is one thing it is variable. As scientists we seek to measure, quantify and explain the causes of this variation. The approach we take to this is remarkably similar whether our research is exploring global temperature, blood pressure, cancer incidence or enzyme kinetics. This approach involves defining clear research questions and applying statistical methods to answer them robustly. This article will introduce a practical example that will be used throughout, specifically whether genetic variation can explain variation in coffee consumption. We assume little experience with statistics and walk through the statistical approach that biologists can use, firstly by describing our data with summary statistics and then by using statistical tests to help arrive at answers to our research question. A General Linear Model (GLM) approach will be used as this is what many common statistical tests are. We explore how to visualise and report results, while checking the assumptions of our analysis. The better we can understand and apply statistics to biological problems, the better we can communicate results and future research to others. The popular statistical programming language R will be used throughout.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 7","pages":"1015-1035"},"PeriodicalIF":6.4,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50157415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

De novo priming: driver of immunotherapy responses or epiphenomenon? 从头引发：免疫疗法反应的驱动因素还是副现象？

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-09-28 DOI: 10.1042/EBC20220244

Alexander L Young, Tara Lorimer, Sarwah K Al-Khalidi, Edward W Roberts

{"title":"De novo priming: driver of immunotherapy responses or epiphenomenon?","authors":"Alexander L Young, Tara Lorimer, Sarwah K Al-Khalidi, Edward W Roberts","doi":"10.1042/EBC20220244","DOIUrl":"10.1042/EBC20220244","url":null,"abstract":"The introduction of immunotherapy, in particular immune checkpoint inhibition, has revolutionised the treatment of a range of tumours; however, only a minority of patients respond to these therapies. Understanding the mechanisms by which different immune checkpoint inhibitors work will be critical for both predicting patients who will respond and to developing rational combination therapies to extend these benefits further. The initiation and maintenance of anti-tumour T cell responses is a complicated process split between both the tumour microenvironment and the tumour draining lymph node. As understanding of this process has increased, it has become apparent that immune checkpoint inhibitors can act both within the tumour and in the draining lymph node and that they can target both already activated T cells as well as stimulating the priming of novel T cell clones. Currently, it seems likely that immune checkpoint inhibition acts both within the tumour and in the tumour draining lymph node both reinvigorating existing clones and driving further de novo priming of novel clones. The relative contributions of these sites and targets may depend on the type of model being used and the timeline of the response. Shorter models emphasise the effect of reinvigoration in the absence of recruitment of new clones but studies spanning longer time periods examining T cell clones in patients demonstrate clonal replacement. Ultimately, further work is needed to determine which of the diverse effects of immune checkpoint inhibitors are the fundamental drivers of anti-tumour responses in patients.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"929-939"},"PeriodicalIF":6.4,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9461636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Immuno-oncology. 免疫肿瘤学。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-09-28 DOI: 10.1042/EBC20230071

Awen Gallimore, Cathy Tournier

{"title":"Immuno-oncology.","authors":"Awen Gallimore, Cathy Tournier","doi":"10.1042/EBC20230071","DOIUrl":"https://doi.org/10.1042/EBC20230071","url":null,"abstract":"Today, it is accepted that the ability to evade the attention of the immune system is an essential hallmark of cancer. Critically, as tumours progress, cancer cells can protect themselves from the immune system's natural ability to fight the disease. This observation has led to an explosion of basic research to discover how to restore anti-tumour immunity for advancing cancer treatment. Clinical successes have been achieved following the approval of checkpoint inhibitor therapy to effectively prolong the life of many cancer patients with malignant disease. However, despite impressive survival gains, there is still a high variability of responses between different types of cancer and many patients still fail to respond. The disappointing findings that have been documented over the many clinical trials performed so far coincide with a much more complex view of immuno-oncology that has emerged from technological advances in functional fluorescent imaging techniques, high-throughput RNA sequencing and single-cell mass cytometry. The themed topic 'Immuno-Oncology' captures the contemporary understanding that individual tumours comprise remarkable mixtures of immune cell populations that actively contribute to neoplastic growth, invasion and metastasis through reciprocal and dynamic interactions with cancer cells. In the context of this new knowledge, the reviews discuss novel ideas of therapeutic opportunities for cancer. We would like to thank the authors for their excellent contributions.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 6","pages":"903"},"PeriodicalIF":6.4,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41119643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Harnessing neutrophil plasticity for HCC immunotherapy. 利用中性粒细胞可塑性进行HCC免疫治疗。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-09-28 DOI: 10.1042/EBC20220245

Erik Ramon-Gil, Daniel Geh, Jack Leslie

{"title":"Harnessing neutrophil plasticity for HCC immunotherapy.","authors":"Erik Ramon-Gil, Daniel Geh, Jack Leslie","doi":"10.1042/EBC20220245","DOIUrl":"10.1042/EBC20220245","url":null,"abstract":"Neutrophils, until recently, have typically been considered a homogeneous population of terminally differentiated cells with highly conserved functions in homeostasis and disease. In hepatocellular carcinoma (HCC), tumour-associated neutrophils (TANs) are predominantly thought to play a pro-tumour role, promoting all aspects of HCC development and progression. Recent developments in single-cell technologies are now providing a greater insight and appreciation for the level of cellular heterogeneity displayed by TANs in the HCC tumour microenvironment, which we have been able to correlate with other TAN signatures in datasets for gastric cancer, pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer (NSCLC). TANs with classical pro-tumour signatures have been identified as well as neutrophils primed for anti-tumour functions that, if activated and expanded, could become a potential therapeutic approach. In recent years, therapeutic targeting of neutrophils in HCC has been typically focused on impairing the recruitment of pro-tumour neutrophils. This has now been coupled with immune checkpoint blockade with the aim to stimulate lymphocyte-mediated anti-tumour immunity whilst impairing neutrophil-mediated immunosuppression. As a result, neutrophil-directed therapies are now entering clinical trials for HCC. Pharmacological targeting along with ex vivo reprogramming of neutrophils in HCC patients is, however, in its infancy and a greater understanding of neutrophil heterogeneity, with a view to exploit it, may pave the way for improved immunotherapy outcomes. This review will cover the recent developments in our understanding of neutrophil heterogeneity in HCC and how neutrophils can be harnessed to improve HCC immunotherapy.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"941-955"},"PeriodicalIF":6.4,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10284679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of IFN-γ-signalling in response to immune checkpoint blockade therapy. IFN-γ信号传导在免疫检查点阻断治疗中的作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-09-28 DOI: 10.1042/EBC20230001

Chun Wai Wong, Yang Yu Huang, Adam Hurlstone

引用次数: 0

T-cell response to checkpoint blockade immunotherapies: from fundamental mechanisms to treatment signatures. T细胞对检查点阻断免疫疗法的反应：从基本机制到治疗特征。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2023-09-28 DOI: 10.1042/EBC20220247

Thomas A E Elliot, David A J Lecky, David Bending

{"title":"T-cell response to checkpoint blockade immunotherapies: from fundamental mechanisms to treatment signatures.","authors":"Thomas A E Elliot, David A J Lecky, David Bending","doi":"10.1042/EBC20220247","DOIUrl":"10.1042/EBC20220247","url":null,"abstract":"Immune checkpoint immunotherapies act to block inhibitory receptors on the surface of T cells and other cells of the immune system. This can increase activation of immune cells and promote tumour clearance. Whilst this is very effective in some types of cancer, significant proportions of patients do not respond to single-agent immunotherapy. To improve patient outcomes, we must first mechanistically understand what drives therapy resistance. Many studies have utilised genetic, transcriptional, and histological signatures to find correlates of effective responses to treatment. It is key that we understand pretreatment predictors of response, but also to understand how the immune system becomes treatment resistant during therapy. Here, we review our understanding of the T-cell signatures that are critical for response, how these immune signatures change during treatment, and how this information can be used to rationally design therapeutic strategies. We highlight how chronic antigen recognition drives heterogeneous T-cell exhaustion and the role of T-cell receptor (TCR) signal strength in exhausted T-cell differentiation and molecular response to therapy. We explore how dynamic changes in negative feedback pathways can promote resistance to single-agent therapy. We speculate that this resistance may be circumvented in the future through identifying the most effective combinations of immunotherapies to promote sustained and durable antitumour responses.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"967-977"},"PeriodicalIF":5.6,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9699152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0