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1.
Methods Mol Biol ; 2449: 3-25, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35507257

RESUMO

With the evermore emphasis put on open science and its invaluable benefits to the scientific community, it is no longer the case where a research project simply ends with a scientific publication. The benefits of data sharing and reproducibility of results have taken the centerpiece within the life science research supported by FAIR principles that firmly underline the importance of open data. The current data-intensive multidisciplinary research has also highlighted the significance of how data is mined and managed. Here we describe some of the features adopted by EMBL-EBI data resources to support data mining, data quality, and data management. We also highlight how EMBL-EBI has responded to the current pandemic through its data resources.


Assuntos
Disciplinas das Ciências Biológicas , Gerenciamento de Dados , Mineração de Dados , Disseminação de Informação , Reprodutibilidade dos Testes
2.
CBE Life Sci Educ ; 21(2): ar32, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35499822

RESUMO

Individuals with disabilities are underrepresented in postsecondary science education and in science careers, yet few studies have explored why this may be. A primary predictor of student persistence in science is participating in undergraduate research. However, it is unclear to what extent students with disabilities are participating in research and what the experiences of these students in research are. To address this gap in the literature, in study 1, we conducted a national survey of more than 1200 undergraduate researchers to determine the percent of students with disabilities participating in undergraduate research in the life sciences. We found that 12% of undergraduate researchers we surveyed self-identified as having a disability, which indicates that students with disabilities are likely underrepresented in undergraduate research. In study 2, we conducted semistructured interviews with 20 undergraduate researchers with disabilities. We identified unique challenges experienced by students with disabilities in undergraduate research, as well as some possible solutions to these challenges. Further, we found that students with disabilities perceived that they provide unique contributions to the research community. This work provides a foundation for creating undergraduate research experiences that are more accessible and inclusive for students with disabilities.


Assuntos
Disciplinas das Ciências Biológicas , Pessoas com Deficiência , Humanos , Pesquisadores , Estudantes
3.
Langmuir ; 38(18): 5323-5338, 2022 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-35483044

RESUMO

In this feature article, we provide an overview of our research on statistical copolymers as a coating material for metal oxide nanoparticles and surfaces. These copolymers contain functional groups enabling noncovalent binding to oxide surfaces and poly(ethylene glycol) (PEG) polymers for colloidal stability and stealthiness. The functional groups are organic derivatives of phosphorous acid compounds R-H2PO3, also known as phosphonic acids that have been screened for their strong affinity to metals and for their multidentate binding ability. Herein we develop a polymer-based coating platform that shares features with the self-assembled monolayer (SAM) and layer-by-layer (L-b-L) deposition techniques. The milestones of this endeavor are the synthesis of PEG-based copolymers containing multiple phosphonic acid groups, the implementation of simple protocols combining versatility with high particle production yields, and the experimental evidence of the colloidal stability of the coated particles. As a demonstration, coating studies are conducted on cerium (CeO2), iron (γ-Fe2O3), aluminum (Al2O3), and titanium (TiO2) oxides of different sizes and morphologies. We finally discuss applications in the domain of nanomaterials and nanomedicine. We evaluate the beneficial effects of coatings on redispersible nanopowders, contrast agents for in vitro/vivo assays, and stimuli-responsive particles.


Assuntos
Disciplinas das Ciências Biológicas , Cério , Nanopartículas Metálicas , Cério/química , Nanopartículas Metálicas/química , Óxidos , Polietilenoglicóis/química , Polímeros/química
4.
Toxins (Basel) ; 14(3)2022 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-35324681

RESUMO

Saporin is a ribosome-inactivating protein that can cause inhibition of protein synthesis and causes cell death when delivered inside a cell. Development of commercial Saporin results in a technology termed 'molecular surgery', with Saporin as the scalpel. Its low toxicity (it has no efficient method of cell entry) and sturdy structure make Saporin a safe and simple molecule for many purposes. The most popular applications use experimental molecules that deliver Saporin via an add-on targeting molecule. These add-ons come in several forms: peptides, protein ligands, antibodies, even DNA fragments that mimic cell-binding ligands. Cells that do not express the targeted cell surface marker will not be affected. This review will highlight some newer efforts and discuss significant and unexpected impacts on science that molecular surgery has yielded over the last almost four decades. There are remarkable changes in fields such as the Neurosciences with models for Alzheimer's Disease and epilepsy, and game-changing effects in the study of pain and itch. Many other uses are also discussed to record the wide-reaching impact of Saporin in research and drug development.


Assuntos
Disciplinas das Ciências Biológicas , Imunotoxinas , Indicadores e Reagentes , Ligantes , N-Glicosil Hidrolases , Proteínas de Plantas/farmacologia , Proteínas Inativadoras de Ribossomos Tipo 1/farmacologia , Saporinas
6.
Biochem Soc Trans ; 50(2): 649-663, 2022 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-35257156

RESUMO

In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.


Assuntos
Disciplinas das Ciências Biológicas , Imageamento Tridimensional , Imageamento Tridimensional/métodos , Microscopia de Fluorescência/métodos , Síncrotrons , Tomografia por Raios X/métodos
7.
Lab Chip ; 22(8): 1415-1437, 2022 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-35348555

RESUMO

Hydrodynamic phenomena can be leveraged to confine a range of biological and chemical species without needing physical walls. In this review, we list methods for the generation and manipulation of microfluidic hydrodynamic confinements in free-flowing liquids and near surfaces, and elucidate the associated underlying theory and discuss their utility in the emerging area of open space microfluidics applied to life-sciences. Microscale hydrodynamic confinements are already starting to transform approaches in fundamental and applied life-sciences research from precise separation and sorting of individual cells, allowing localized bio-printing to multiplexing for clinical diagnosis. Through the choice of specific flow regimes and geometrical boundary conditions, hydrodynamic confinements can confine species across different length scales from small molecules to large cells, and thus be applied to a wide range of functionalities. We here provide practical examples and implementations for the formation of these confinements in different boundary conditions - within closed channels, in between parallel plates and in an open liquid volume. Further, to enable non-microfluidics researchers to apply hydrodynamic flow confinements in their work, we provide simplified instructions pertaining to their design and modelling, as well as to the formation of hydrodynamic flow confinements in the form of step-by-step tutorials and analytical toolbox software. This review is written with the idea to lower the barrier towards the use of hydrodynamic flow confinements in life sciences research.


Assuntos
Disciplinas das Ciências Biológicas , Técnicas Analíticas Microfluídicas , Hidrodinâmica , Técnicas Analíticas Microfluídicas/métodos , Microfluídica/métodos , Software
8.
CBE Life Sci Educ ; 21(2): ar18, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35294254

RESUMO

Depression is one of the top mental health concerns among undergraduates and disproportionately affects students who are underrepresented in science. As such, understanding how emerging science learning environments, such as online science courses, affect students with depression is integral to creating a more inclusive scientific community. In this exploratory study, we interviewed 24 undergraduates with depression who were pursuing an online BS degree in biological sciences at a research-intensive institution. We assessed how students perceived depression affected their learning, and in turn, how online science courses affected their depression. Using a hybrid approach of deductive and inductive coding, we found that students reported depression negatively affected an array of cognitive domains when learning science online, including students' effort, focus, and time management. Students reported that the fast pace of online courses, the lack of needing to show up to a class in person, and difficulty developing relationships with other students commonly exacerbated their depression. Conversely, the flexibility of completing course work when and where students wanted, developing a relationship with the instructor, and the ease of having questions answered online positively affected students' depression. This study provides insight into ways to create inclusive online learning environments for students with depression.


Assuntos
Disciplinas das Ciências Biológicas , Educação à Distância , Depressão , Humanos , Estudantes/psicologia
9.
J Synchrotron Radiat ; 29(Pt 2): 540-548, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-35254319

RESUMO

This work describes the instrumentation and software for microbeam scattering and structural mapping at the Life Science X-ray Scattering (LiX) beamline at NSLS-II. Using a two-stage focusing scheme, an adjustable beam size between a few micrometres and a fraction of a millimetre is produced at the sample position. Scattering data at small and wide angles are collected simultaneously on multiple Pilatus detectors. A recent addition of an in-vacuum Pilatus 900k detector, with the detector modules arranged in a C-shaped configuration, has improved the azimuthal angle coverage in the wide-angle data. As an option, fluorescence data can be collected simultaneously. Fly scans have been implemented to minimize the time interval between scattering patterns and to avoid unnecessary radiation damage to the sample. For weakly scattering samples, an in-vacuum sample environment has been developed here to minimize background scattering. Data processing for these measurements is highly sample-specific. To establish a generalized data process workflow, first the data are reduced to reciprocal coordinates at the time of data collection. The users can then quantify features of their choosing from these intermediate data and construct structural maps. As examples, results from in-vacuum mapping of onion epidermal cell walls and 2D tomographic sectioning of an intact poplar stem are presented.


Assuntos
Disciplinas das Ciências Biológicas , Síncrotrons , Espalhamento a Baixo Ângulo , Difração de Raios X , Raios X
10.
Microscopy (Oxf) ; 71(Supplement_1): i3-i14, 2022 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-35275178

RESUMO

The three-dimensional structure of biological macromolecules, such as proteins and nucleic acids, and their complexes is the fundamental information not only for life sciences but also for medical sciences and drug design. Electron cryomicroscopy has become an extremely powerful tool for high-resolution structural analysis of biological macromolecules, not just in addition to X-ray crystallography and nuclear magnetic resonance sepectroscopy (NMR) that have been used as the basic techniques in structural biology. By the development of hardware and software, such as transmission electron cryomicroscopes with highly stable and controllable electron optics, cold field emission gun and energy filter, complementary metal oxide semiconductor (CMOS)-based direct electron detectors with high frame rate and high sensitivity, high-speed computers and software programs for image analysis, electron cryomicroscopy now allows structure determination of biological macromolecules at atomic levels within a few days even from a drop of solution sample with an amount as small as a few micrograms. How can the structures of macromolecules be imaged and analyzed at atomic level resolution in their native states despite their high sensitivity to radiation damage at a relatively low level of electron irradiation? We describe recent progress and future perspective of electron cryomicroscopy for structural life sciences.


Assuntos
Disciplinas das Ciências Biológicas , Processamento de Imagem Assistida por Computador , Microscopia Crioeletrônica/métodos , Cristalografia por Raios X , Processamento de Imagem Assistida por Computador/métodos , Substâncias Macromoleculares/química
11.
PLoS One ; 17(2): e0263001, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35139089

RESUMO

The COVID-19 outbreak has posed an unprecedented challenge to humanity and science. On the one side, public and private incentives have been put in place to promptly allocate resources toward research areas strictly related to the COVID-19 emergency. However, research in many fields not directly related to the pandemic has been displaced. In this paper, we assess the impact of COVID-19 on world scientific production in the life sciences and find indications that the usage of medical subject headings (MeSH) has changed following the outbreak. We estimate through a difference-in-differences approach the impact of the start of the COVID-19 pandemic on scientific production using the PubMed database (3.6 Million research papers). We find that COVID-19-related MeSH terms have experienced a 6.5 fold increase in output on average, while publications on unrelated MeSH terms dropped by 10 to 12%. The publication weighted impact has an even more pronounced negative effect (-16% to -19%). Moreover, COVID-19 has displaced clinical trial publications (-24%) and diverted grants from research areas not closely related to COVID-19. Note that since COVID-19 publications may have been fast-tracked, the sudden surge in COVID-19 publications might be driven by editorial policy.


Assuntos
Pesquisa Biomédica , COVID-19 , Bibliometria , Disciplinas das Ciências Biológicas , COVID-19/epidemiologia , Humanos , Medical Subject Headings , PubMed
12.
PLoS One ; 17(2): e0263185, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35108316

RESUMO

Discussions about science and engineering postdoctoral researchers focus almost exclusively on academic postdocs and their chances of eventually securing tenure-track faculty positions. Further, biological sciences dominate policy research and published advice for new PhDs regarding postdoctoral employment. Our analysis uses the Survey of Earned Doctorates and Survey of Doctorate Recipients to understand employment implications for physical sciences and engineering (PSE) and life sciences (LS) graduates who took postdoctoral positions in government, industry, and academic sectors. We examine postdoc duration, reasons for staying in a postdoc, movement between sectors, and salary implications. There is considerable movement between employment sectors within the first six years post-PhD. Additionally, postdocs in PSE are shorter, better paid, and more often in nonacademic sectors than postdocs in LS. These results can help science and engineering faculty discuss a broader range of career pathways with doctoral students and help new PhDs make better informed early career decisions.


Assuntos
Pesquisa Biomédica/educação , Escolha da Profissão , Emprego , Engenharia/educação , Disciplinas das Ciências Naturais/educação , Pesquisadores/educação , Academias e Institutos/estatística & dados numéricos , Disciplinas das Ciências Biológicas/educação , Educação de Pós-Graduação , Feminino , Governo , Humanos , Indústrias/estatística & dados numéricos , Masculino , Estados Unidos
13.
BMC Bioinformatics ; 23(1): 61, 2022 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-35130839

RESUMO

BACKGROUND: As technical developments in omics and biomedical imaging increase the throughput of data generation in life sciences, the need for information systems capable of managing heterogeneous digital assets is increasing. In particular, systems supporting the findability, accessibility, interoperability, and reusability (FAIR) principles of scientific data management. RESULTS: We propose a Service Oriented Architecture approach for integrated management and analysis of multi-omics and biomedical imaging data. Our architecture introduces an image management system into a FAIR-supporting, web-based platform for omics data management. Interoperable metadata models and middleware components implement the required data management operations. The resulting architecture allows for FAIR management of omics and imaging data, facilitating metadata queries from software applications. The applicability of the proposed architecture is demonstrated using two technical proofs of concept and a use case, aimed at molecular plant biology and clinical liver cancer research, which integrate various imaging and omics modalities. CONCLUSIONS: We describe a data management architecture for integrated, FAIR-supporting management of omics and biomedical imaging data, and exemplify its applicability for basic biology research and clinical studies. We anticipate that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, including studies which leverage advanced machine learning methods, as the joint analysis of omics and imaging data, in conjunction with phenotypic metadata, becomes not only desirable but necessary to derive novel insights into biological processes.


Assuntos
Disciplinas das Ciências Biológicas , Gerenciamento de Dados , Gestão da Informação , Metadados , Software
14.
Drug Discov Today ; 27(5): 1441-1447, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35066138

RESUMO

Over recent years, there has been exciting growth in collaboration between academia and industry in the life sciences to make data more Findable, Accessible, Interoperable and Reusable (FAIR) to achieve greater value. Despite considerable progress, the transformative shift from an application-centric to a data-centric perspective, enabled by FAIR implementation, remains very much a work in progress on the 'FAIR journey'. In this review, we consider use cases for FAIR implementation. These can be deployed alongside assessment of data quality to maximize the value of data generated from research, clinical trials, and real-world healthcare data, which are essential for the discovery and development of new medical treatments by biopharma.


Assuntos
Disciplinas das Ciências Biológicas , Confiabilidade dos Dados , Indústrias
17.
Cell ; 185(2): 224-226, 2022 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-35063068

RESUMO

Elle Lett is the winner of the 2021 Rising Black Scientists Award for a post-graduate scholar. For this award, we asked emerging Black scientists to tell us about the experiences that sparked their interest in the life sciences, their vision and goals, and how they want to contribute to a more inclusive scientific community. This is her story.


Assuntos
Disciplinas das Ciências Biológicas , Bioestatística , Pessoal de Laboratório Médico/psicologia , Justiça Social , Pessoas Transgênero/psicologia , Distinções e Prêmios , Educação de Pós-Graduação , Feminino , Objetivos , Humanos , Racismo/psicologia
18.
PLoS One ; 17(1): e0262615, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35041695

RESUMO

Although several studies have been conducted to summarize the progress of open educational resources (OER) in specific regions, only a limited number of studies summarize OER in Africa. Therefore, this paper presents a systematic literature review to explore trends, themes, and patterns in this emerging area of study, using content and bibliometric analysis. Findings indicated three major strands of OER research in Africa: (1) OER adoption is only limited to specific African countries, calling for more research and collaboration between African countries in this field to ensure educational equity; (2) most of the OER initiatives in Africa have focused on the creation process and neglected other important perspectives, such as dissemination and open educational practices (OEP) using OER; and (3) on top of the typical challenges for OER adoption (e.g., infrastructure), other personal challenges were identified within the African context, including culture, language, and personality. The findings of this study suggest that more initiatives and cross-collaborations with African and non-African countries in the field of OER are needed to facilitate OER adoption in the region. Additionally, it is suggested that researchers and practitioners should consider individual differences, such as language, personality and culture, when promoting and designing OER for different African countries. Finally, the findings can promote social justice by providing insights and future research paths that different stakeholders (e.g., policy makers, educators, practitioners, etc.) should focus on to promote OER in Africa.


Assuntos
Disciplinas das Ciências Biológicas/educação , Biologia Computacional/normas , Educação à Distância/normas , Pesquisadores/educação , África , Bibliometria , Humanos , Pesquisadores/estatística & dados numéricos
19.
Semina cienc. biol. saude ; 43(1): 129-152, jan./jun. 2022. ilus, tab
Artigo em Inglês | LILACS | ID: biblio-1354470

RESUMO

This macro-level scientometrics study aimed to analyze the similarities and differences in the scientific communication patterns of the Brazilian postgraduate programs (BPPs) belonging to the Biological Sciences II field (BS2), as defined by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). Also, it was identified the most researched diseases and it was discussed their relationship with the needs of Brazilian public health considering the burden of disease (Disability-Adjusted Life Year - DALY, Brazil) estimated by the World Health Organization (WHO). Thus, the scientific production of the BS2's sub-areas Biophysics, Biochemistry, Pharmacology, Physiology, and Morphology was evaluated from 2013 to 2016, through considering the citation impact, Impact Factor (Journal Citation Reports), and scientific collaboration. Data collected included formal information provided to CAPES by all BPPs through the Plataforma Sucupira as well as metadata from Web of Science documents. In addition, were employed the standardized Medical Subject Headings (PubMed) for the analysis of researched diseases. We concluded that the patterns of scientific communication in Biophysics, Biochemistry, Pharmacology, Physiology, and Morphology were predominantly different. Thus, there is a need to consider specificities among the five sub-areas in the evaluation process performed by CAPES. Different approaches are revealed by identifying the most frequently researched diseases and explaining the contributions of each sub-area for Brazilian public health.


Este estudo cientométrico de nível macro teve como objetivo analisar as semelhanças e as diferenças nos padrões de comunicação científica dos programas de pós-graduação brasileiros (PPGs) da área de Ciências Biológicas II, avaliados pela Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). Além disso, foram identificadas as doenças mais pesquisadas e foi discutido sua relação com as necessidades de saúde pública brasileira, considerando a carga de doenças (Disability-Adjusted Life Year - DALY, Brasil) estimada pela Organização Mundial da Saúde (OMS). Assim, a produção científica das subáreas Biofísica, Bioquímica, Farmacologia, Fisiologia e Morfologia da área de Ciências Biológicas II foi avaliada de 2013 a 2016, considerando o impacto de citações, o Fator de Impacto (Journal Citation Reports) e a colaboração científica. Os dados coletados incluíram informações declaradas à CAPES por todos os PPGs por meio da Plataforma Sucupira, bem como metadados de documentos da Web of Science. Além disso, foram utilizados os cabeçalhos de Medical Subject Headings (PubMed) para a análise das doenças pesquisadas. Concluímos que os padrões de comunicação científica entre as subáreas Biofísica, Bioquímica, Farmacologia, Fisiologia e Morfologia foram predominantemente diferentes. Assim, é necessário considerar as especificidades entre as cinco subáreas no processo de avaliação realizado pela CAPES. Diferentes abordagens são reveladas a partir da identificação das doenças mais pesquisadas e da explicação das contribuições de cada subárea para a saúde pública brasileira.


Assuntos
Humanos , Organização Mundial da Saúde , Disciplinas das Ciências Biológicas , Medical Subject Headings , Fator de Impacto , Metadados , Pós , Bioquímica , Biofísica , Saúde Pública , PubMed
20.
FEBS J ; 289(4): 858-860, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34689410

RESUMO

Every quarter, The FEBS Journal presents some of its 'hidden gems'-original research and review-type articles that provide a significant advance or discuss recent developments in the molecular or cellular life sciences. These articles are of high value to the scientific community, and we like to take the opportunity to promote these contributions from previous issues of the journal, as we feel their scientific content merits a boost in exposure.


Assuntos
Disciplinas das Ciências Biológicas , Editoração , Humanos
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