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Canadian Journal of Gastroenterology &... 2018
Topics: Biomarkers, Tumor; Epigenesis, Genetic; Gastrointestinal Neoplasms; Humans; Molecular Biology
PubMed: 30941325
DOI: 10.1155/2018/4513860 -
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic Acids Research Jan 2021The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new...
The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.
Topics: COVID-19; Computational Biology; Databases, Nucleic Acid; Epidemics; Genomics; Humans; Internet; Molecular Biology; Nucleic Acids; Periodicals as Topic; Research; SARS-CoV-2
PubMed: 33396976
DOI: 10.1093/nar/gkaa1216 -
ELife Jul 2016In vitro selection of antibodies allows to obtain highly functional binders, rapidly and at lower cost. Here, we describe the first fully synthetic phage display library...
In vitro selection of antibodies allows to obtain highly functional binders, rapidly and at lower cost. Here, we describe the first fully synthetic phage display library of humanized llama single domain antibody (NaLi-H1: Nanobody Library Humanized 1). Based on a humanized synthetic single domain antibody (hs2dAb) scaffold optimized for intracellular stability, the highly diverse library provides high affinity binders without animal immunization. NaLi-H1 was screened following several selection schemes against various targets (Fluorescent proteins, actin, tubulin, p53, HP1). Conformation antibodies against active RHO GTPase were also obtained. Selected hs2dAb were used in various immunoassays and were often found to be functional intrabodies, enabling tracking or inhibition of endogenous targets. Functionalization of intrabodies allowed specific protein knockdown in living cells. Finally, direct selection against the surface of tumor cells produced hs2dAb directed against tumor-specific antigens further highlighting the potential use of this library for therapeutic applications.
Topics: Animals; Antibodies, Monoclonal, Humanized; Camelids, New World; Humans; Molecular Biology; Peptide Library; Single-Domain Antibodies
PubMed: 27434673
DOI: 10.7554/eLife.16228 -
International Journal of Molecular... Nov 2023Flow cytometry is a single-cell based technology aimed to quantify the scattering of light and the emission of multiple fluorescence signals by individual cells,...
Flow cytometry is a single-cell based technology aimed to quantify the scattering of light and the emission of multiple fluorescence signals by individual cells, biological vesicles, or synthetic microscopical particles when examined one by one at high speed using lasers or other suitable illumination sources [...].
Topics: Flow Cytometry; Molecular Biology
PubMed: 38003405
DOI: 10.3390/ijms242216215 -
International Journal of Molecular... Mar 2023Neurological disorders are a large and heterogeneous field of research that can be tackled through a variety of approaches, ranging from epidemiology to molecular...
Neurological disorders are a large and heterogeneous field of research that can be tackled through a variety of approaches, ranging from epidemiology to molecular biology, through clinical, biostatistical, and laboratory experiments [...].
Topics: Humans; Nervous System Diseases; Molecular Biology; Laboratories
PubMed: 36982976
DOI: 10.3390/ijms24065902 -
Journal of Integrative Bioinformatics May 2019Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing...
Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand of scientists with a combined background in both fields, the education of dry and wet lab subjects are often still separated. This work describes an example of integrated education with a focus on genomics and transcriptomics. Participants learned computational and molecular biology methods in the same practical course. Peer-review was applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. The positive evaluation results indicate that this approach was accepted by the participants and would likely be suitable for wider scale application.
Topics: Computational Biology; Female; Humans; Male; Molecular Biology
PubMed: 31145692
DOI: 10.1515/jib-2019-0005 -
Molecular Neurodegeneration Sep 2014The field of neurodegeneration research has been advancing rapidly over the past few years, and has provided intriguing new insights into the normal physiological...
The field of neurodegeneration research has been advancing rapidly over the past few years, and has provided intriguing new insights into the normal physiological functions and pathogenic roles of a wide range of molecules associated with several devastating neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, and Down syndrome. Recent developments have also facilitated initial efforts to translate preclinical discoveries toward novel therapeutic approaches and clinical trials in humans. These recent developments are reviewed in the current Review Series on "Molecular Neurodegeneration: Basic Biology and Disease Pathways" in a number of state-of-the-art manuscripts that cover themes presented at the Third International Conference on Molecular Neurodegeneration: "Basic biology and disease pathways" held in Cannes, France, September, 2013.
Topics: Animals; Humans; Molecular Biology; Nerve Degeneration; Neurodegenerative Diseases
PubMed: 25248568
DOI: 10.1186/1750-1326-9-34 -
FEBS Open Bio Feb 2021
Topics: Biomedical Research; Europe; Female; Genomics; History, 20th Century; History, 21st Century; Humans; Metabolomics; Molecular Biology; Research Personnel; Societies, Scientific
PubMed: 33611861
DOI: 10.1002/2211-5463.13077 -
Nature Protocols Nov 2015Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate...
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs. This protocol describes the experimental steps, implemented over 3 d, that are required to perform SHAPE probing and to construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots and provides useful troubleshooting information. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures and visualize probable and alternative helices, often in under 1 d. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and entire transcriptomes.
Topics: Acylation; Computational Biology; Models, Molecular; Molecular Biology; Mutation; Nucleic Acid Conformation; RNA; RNA Processing, Post-Transcriptional
PubMed: 26426499
DOI: 10.1038/nprot.2015.103 -
Trends in Cell Biology Jul 2020The driving passion of molecular cell biologists is to understand the molecular mechanisms that control important aspects of cell physiology, but this ambition is often... (Review)
Review
The driving passion of molecular cell biologists is to understand the molecular mechanisms that control important aspects of cell physiology, but this ambition is often limited by the wealth of molecular details currently known about these mechanisms. Their complexity overwhelms our intuitive notions of how molecular regulatory networks might respond under normal and stressful conditions. To make progress we need a new paradigm for connecting molecular biology to cell physiology. We suggest an approach that uses precise mathematical methods to associate the qualitative features of dynamical systems, as conveyed by 'bifurcation diagrams', with 'signal-response' curves measured by cell biologists.
Topics: Cell Biology; Circadian Rhythm; Models, Biological; Molecular Biology
PubMed: 32362451
DOI: 10.1016/j.tcb.2020.04.002