Essays in biochemistry最新文献_第7页

Innovate and empower: the malate dehydrogenase course-based undergraduate research experiences and community of practice. 创新和赋权：基于苹果酸脱氢酶课程的本科生研究经验和实践社区。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230074

Sue Ellen DeChenne-Peters, Nicole L Scheuermann, Amy D Parente, Jing Zhang

{"title":"Innovate and empower: the malate dehydrogenase course-based undergraduate research experiences and community of practice.","authors":"Sue Ellen DeChenne-Peters, Nicole L Scheuermann, Amy D Parente, Jing Zhang","doi":"10.1042/EBC20230074","DOIUrl":"10.1042/EBC20230074","url":null,"abstract":"College science programs exhibit high rates of student attrition, especially among Students of Color, women, members of the LGBTQ+ community, and those with disabilities. Many of the reasons students choose to leave or feel pushed out of science can be mitigated through participation in faculty-mentored research. However, faculty resources are limited, and not every student has access to faculty mentoring due to systemic or structural barriers. By bringing authentic scientific research into the classroom context, course-based undergraduate research experiences (CUREs) expand the number of students who participate in research and provide benefits similar to faculty-mentored research. Instructors also benefit from teaching CUREs. Using a systematic review of 14 manuscripts concerning the Malate Dehydrogenase CUREs Community (MCC) and malate dehydrogenase (MDH) CUREs, we demonstrate that CUREs can be implemented flexibly, are authentic research experiences, generate new scientific discoveries, and improve student outcomes. Additionally, CURE communities offer substantial advantages to faculty wishing to implement CUREs.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"253-268"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733833","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

The structural biology and dynamics of malate dehydrogenases. 苹果酸脱氢酶的结构生物学和动力学。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230082

Christopher E Berndsen, Jessica K Bell

{"title":"The structural biology and dynamics of malate dehydrogenases.","authors":"Christopher E Berndsen, Jessica K Bell","doi":"10.1042/EBC20230082","DOIUrl":"10.1042/EBC20230082","url":null,"abstract":"Malate dehydrogenase (MDH) enzymes catalyze the reversible oxidoreduction of malate to oxaloacetate using NAD(P) as a cofactor. This reaction is vital for metabolism and the exchange of reducing equivalents between cellular compartments. There are more than 100 structures of MDH in the Protein Data Bank, representing species from archaea, bacteria, and eukaryotes. This conserved family of enzymes shares a common nucleotide-binding domain, substrate-binding domain, and subunits associate to form a dimeric or a tetrameric enzyme. Despite the variety of crystallization conditions and ligands in the experimental structures, the conformation and configuration of MDH are similar. The quaternary structure and active site dynamics account for most conformational differences in the experimental MDH structures. Oligomerization appears essential for activity despite each subunit having a structurally independent active site. There are two dynamic regions within the active site that influence substrate binding and possibly catalysis, with one of these regions adjoining the subunit interface. In this review, we introduce the reader to the general structural framework of MDH highlighting the conservation of certain features and pointing out unique differences that regulate MDH enzyme activity.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"57-72"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901346","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

Computational models as catalysts for investigating redoxin systems. 计算模型是研究氧化还原系统的催化剂。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-04-30 DOI: 10.1042/EBC20230036

Ché S Pillay, Johann M Rohwer

{"title":"Computational models as catalysts for investigating redoxin systems.","authors":"Ché S Pillay, Johann M Rohwer","doi":"10.1042/EBC20230036","DOIUrl":"10.1042/EBC20230036","url":null,"abstract":"Thioredoxin, glutaredoxin and peroxiredoxin systems play central roles in redox regulation, signaling and metabolism in cells. In these systems, reducing equivalents from NAD(P)H are transferred by coupled thiol-disulfide exchange reactions to redoxins which then reduce a wide array of targets. However, the characterization of redoxin activity has been unclear, with redoxins regarded as enzymes in some studies and redox metabolites in others. Consequently, redoxin activities have been quantified by enzyme kinetic parameters in vitro, and redox potentials or redox ratios within cells. By analyzing all the reactions within these systems, computational models showed that many kinetic properties attributed to redoxins were due to system-level effects. Models of cellular redoxin networks have also been used to estimate intracellular hydrogen peroxide levels, analyze redox signaling and couple omic and kinetic data to understand the regulation of these networks in disease. Computational modeling has emerged as a powerful complementary tool to traditional redoxin enzyme kinetic and cellular assays that integrates data from a number of sources into a single quantitative framework to accelerate the analysis of redoxin systems.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"27-39"},"PeriodicalIF":6.4,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734762","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

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

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 5.6 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":5.6,"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