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The potential and pitfalls of large language models in molecular biosciences 大型语言模型在分子生物科学中的潜力和陷阱
The Biochemist Pub Date : 2024-05-16 DOI: 10.1042/bio_2024_121
Chengqi Xu, Olivier Elemento
{"title":"The potential and pitfalls of large language models in molecular biosciences","authors":"Chengqi Xu, Olivier Elemento","doi":"10.1042/bio_2024_121","DOIUrl":"https://doi.org/10.1042/bio_2024_121","url":null,"abstract":"Large language models (LLMs) have revolutionized information processing and are now being applied to complex problems in molecular biosciences. LLMs excel at learning patterns in biological sequences, enabling applications such as predicting the function of DNA regulatory elements, analysing chromatin modifications and predicting the effects of genetic variants. In drug discovery, LLMs are being used to optimize drug properties, design novel molecules and even automate compound synthesis. However, realizing the full potential of LLMs in the molecular biosciences requires addressing challenges such as designing effective learning objectives, generating high-quality, domain-specific datasets and building trust in AI-assisted decision-making. As these challenges are addressed, LLMs hold immense potential for advancing research and driving ground-breaking discoveries in molecular biosciences.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"25 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140968585","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}
引用次数: 0
AI in bioscience education and assessment 生物科学教育和评估中的人工智能
The Biochemist Pub Date : 2024-05-07 DOI: 10.1042/bio_2024_123
David Smith
{"title":"AI in bioscience education and assessment","authors":"David Smith","doi":"10.1042/bio_2024_123","DOIUrl":"https://doi.org/10.1042/bio_2024_123","url":null,"abstract":"The landscape of bioscience education has changed dramatically over the last few years, first due to the COVID pandemic and now with the explosion of artificial intelligence. David Smith, Professor of Bioscience Education at Sheffield Hallam University, discusses some of the bigger questions in relation to the use of AI in bioscience education and assessment.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"126 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141002958","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}
引用次数: 0
Towards equity, diversity, and inclusion in the molecular biosciences: a Biochemical Society position statement 实现分子生物科学的公平、多样性和包容性：生化学会立场声明
The Biochemist Pub Date : 2024-05-07 DOI: 10.1042/bio_2024_114
Orla Lappin, Sarah Jenner, Amanda Marie James, Derry K Mercer
{"title":"Towards equity, diversity, and inclusion in the molecular biosciences: a Biochemical Society position statement","authors":"Orla Lappin, Sarah Jenner, Amanda Marie James, Derry K Mercer","doi":"10.1042/bio_2024_114","DOIUrl":"https://doi.org/10.1042/bio_2024_114","url":null,"abstract":"","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"71 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141003209","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}
引用次数: 0
A beginner’s guide to immunohistochemistry 免疫组化新手指南
The Biochemist Pub Date : 2024-05-03 DOI: 10.1042/bio_2024_112
Majda El Hassani, Cristina Cocco
{"title":"A beginner’s guide to immunohistochemistry","authors":"Majda El Hassani, Cristina Cocco","doi":"10.1042/bio_2024_112","DOIUrl":"https://doi.org/10.1042/bio_2024_112","url":null,"abstract":"Using the affinity between antibodies and antigens, immunohistochemistry (IHC) is a helpful method for analysing the cellular components within tissue sections placed on glass slides. The chemistry of antibodies was not discovered until 1941, and since then, their use has increased due to the discovery of enzymes and fluorochromes conjugated to antibodies, enabling observations through optical or fluorescence microscopy (FM). Hence, immunofluorescence (IF), or IHC with fluorescent antibodies, has been associated with the advancement of FM and fluorochromes. Specifically, the discovery of three fluorochromes that emit blue, red and green led to a rise in IF application in the context of visualizing numerous components in a single cell. The proximity ligation assay (PLA) method, so termed because the antibody is conjugated with short DNA strands called PLA probes, is the most recent development in the field of antibody conjugation. Protein–protein interactions and sub-localization of proteins can both be studied using this technique. The improvement of conjugation techniques has occurred in parallel with the development of sophisticated microscopies, including confocal and slide scanners. Confocal microscopy allows for the reconstruction of three-dimensional structures while a slide scanner can digitally convert up to 100 slides' worth of high-resolution pictures. The first step in the IHC process is the collection and fixation of tissues from animal models and humans. Paraformaldehyde is the most commonly used fixative. Fixation prevents antigen blocking and creates cross-links between proteins to preserve tissue structures. Fixation is followed by cutting tissues using microtome or cryostat, then slides are treated for antigen exposition (antigen retrieval) and then included in Triton X solution, which increases membrane permeability. Subsequently, incubations with enzyme- or fluorochrome-conjugated antibodies enable observations via optical microscopy or FM, respectively. In clinical practice and research, IHC and IF are still helpful methods for identifying the antigen-proteins linked to specific diseases.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"186 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141015162","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}
引用次数: 0
AI told you so: navigating protein structure prediction in the era of machine learning 人工智能告诉你：机器学习时代的蛋白质结构预测导航
The Biochemist Pub Date : 2024-05-03 DOI: 10.1042/bio_2024_118
Sami Chaaban, Giedrė Ratkevičiūtė, Clinton Lau
{"title":"AI told you so: navigating protein structure prediction in the era of machine learning","authors":"Sami Chaaban, Giedrė Ratkevičiūtė, Clinton Lau","doi":"10.1042/bio_2024_118","DOIUrl":"https://doi.org/10.1042/bio_2024_118","url":null,"abstract":"Every protein in our cells has evolved to fold into a specific structure to perform its functions. However, determining these structures experimentally is often challenging, in some cases taking years. Recently, machine-learning algorithms have been designed to predict a protein’s structure directly from its amino acid sequence in minutes to hours. Since the release of the first of these algorithms, AlphaFold and RoseTTAFold, several more have been developed. These have been complemented by tools that leverage the outputs to give structural context to biochemical data, screen for novel protein–protein interactions or even help solve experimental structures. In addition, several public resources have incorporated the predictions into their databases, making the data open to all. Here, we provide a user-focused perspective on machine-learning protein structure prediction, covering some of the popular applications and highlighting caveats. Used effectively, predictive programs offer the potential to speed up research and guide experimental design.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"12 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141014617","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}
引用次数: 0
A day in the life of a chief data science officer and co-founder of Ignota Labs 首席数据科学官兼 Ignota 实验室联合创始人的一天
The Biochemist Pub Date : 2024-05-03 DOI: 10.1042/bio_2024_117
Layla Hosseini-Gerami
{"title":"A day in the life of a chief data science officer and co-founder of Ignota Labs","authors":"Layla Hosseini-Gerami","doi":"10.1042/bio_2024_117","DOIUrl":"https://doi.org/10.1042/bio_2024_117","url":null,"abstract":"Layla is a chief data science officer and co-founder of Ignota Labs. Layla studied chemistry and bioinformatics before co-founding Ignota Labs, which focuses on using explainable AI methods to predict, understand, and turnaround safety issues in drug discovery. Layla gives us an insight into working as a Chief Data Science Officer, transitioning from academia to industry and establishing a business.\u0000","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"1 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141015321","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}
引用次数: 0
Students’ top-10 wish list for inclusive, engaging video lectures 学生对包容性强、引人入胜的视频讲座的十大愿望清单
The Biochemist Pub Date : 2024-04-04 DOI: 10.1042/bio_2024_101
Ellie Davison
{"title":"Students’ top-10 wish list for inclusive, engaging video lectures","authors":"Ellie Davison","doi":"10.1042/bio_2024_101","DOIUrl":"https://doi.org/10.1042/bio_2024_101","url":null,"abstract":"Professor Ellie Davison is the winner of the 2024 Teaching Excellence Award (Established Educator), recognizing innovative and effective teaching approaches that promote achievement for all, with a sustained impact on students and colleagues across the sector. Ellie champions widening participation and inclusive teaching approaches that enable diverse cohorts to thrive. She strives to co-create learning experiences with students as partners, empowered to contribute and learn as their authentic selves.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"4 S3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140741872","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}
引用次数: 0
Could the medicalization of psychedelics lead to the next generation of antidepressants? 迷幻药的医学化会带来下一代抗抑郁药吗？
The Biochemist Pub Date : 2024-03-28 DOI: 10.1042/bio_2023_164
Peter Duggan, Scott Walker
{"title":"Could the medicalization of psychedelics lead to the next generation of antidepressants?","authors":"Peter Duggan, Scott Walker","doi":"10.1042/bio_2023_164","DOIUrl":"https://doi.org/10.1042/bio_2023_164","url":null,"abstract":"A major part of the counterculture that emerged in western societies in the 1960s centred around the use of mind-altering psychedelic drugs such as lysergic acid diethylamide (LSD). Humans had, however, been consuming hallucinogenic substances since prehistoric times and often incorporated them into their religious rituals. Concerns over the effects of potent psychedelics like LSD led to them being outlawed in many jurisdictions around the world via the UN Convention on Psychotropic Substances in 1971. During the intervening decades, the scientific investigation of psychedelics and their potential for legitimate therapeutic use has consequently been limited. In recent years, hints that psychedelics may be effective against certain treatment-resistant depressive states like post-traumatic stress disorder (PSTD) have led to more concerted efforts to obtain reliable clinical data that could convince drug regulators to approve them as legitimate medical treatments.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"104 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140370754","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}
引用次数: 0
Psychedelics: reconnecting the brain to heal the mind 迷幻药：重新连接大脑以治愈心灵
The Biochemist Pub Date : 2024-03-26 DOI: 10.1042/bio_2023_156
David J. Nutt
{"title":"Psychedelics: reconnecting the brain to heal the mind","authors":"David J. Nutt","doi":"10.1042/bio_2023_156","DOIUrl":"https://doi.org/10.1042/bio_2023_156","url":null,"abstract":"Natural psychedelics such as magic mushrooms have a long history of human use of at least 7000 years. Their use underwent a resurgence in the 1950/1960s following the synthesis of LSD as a psychedelic and its use as a medicine with powerful therapeutic benefits. But because non-medical use led to massive cultural changes especially in young people, all psychedelics were banned globally in the early 1970s. Over the past 20 years, there has been a resurrection of psychedelic research. This has revealed their common modes of action as agonists (stimulators) of the serotonin 5-HT2A receptor in the brain and that this activity leads to profound alterations in neuro-circuitry, producing a more integrated and flexible pattern of activity. These brain changes found in healthy volunteers predicted utility in mental illnesses such as depression and addiction and subsequent trials revealed this to be true. A single psychedelic trip can lead to very long-lasting improvements in a range of mental illnesses. From these remarkable and consistent positive outcomes, it seems likely that psychedelic therapy will soon become widely approved in western medicine, as it has already been in Australia for treatment-resistant depression.","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"82 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140377879","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}
引用次数: 0
Psychedelic therapies 迷幻疗法
The Biochemist Pub Date : 2024-03-25 DOI: 10.1042/bio_2024_115
Colin Bingle
{"title":"Psychedelic therapies","authors":"Colin Bingle","doi":"10.1042/bio_2024_115","DOIUrl":"https://doi.org/10.1042/bio_2024_115","url":null,"abstract":"","PeriodicalId":510527,"journal":{"name":"The Biochemist","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140381400","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}
引用次数: 0
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