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Berman, Helen M., Christine Zardecki, and John Westbrook. "The Nucleic Acid Database: A Resource for Nucleic Acid Science." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1095–104. http://dx.doi.org/10.1107/s0907444998007926.
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The Nucleic Acid Database (NDB) distributes information about nucleic acid-containing structures. Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given.
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Peters, Richard, and Robert S. Sikorski. "Nucleic acid databases on the Web." Nature Biotechnology 14, no. 13 (December 1996): 1728. http://dx.doi.org/10.1038/nbt1296-1728.
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Adman, E., M. Gellert, M. Cohen, N. Allewell, B. Baker, and J. Villafranca. "National protein and nucleic acid databases." Science 264, no. 5156 (April 8, 1994): 187. http://dx.doi.org/10.1126/science.7511836.
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Kneale, G. G., and M. J. Bishop. "Nucleic acid and protein sequence databases." Bioinformatics 1, no. 1 (1985): 11–17. http://dx.doi.org/10.1093/bioinformatics/1.1.11.
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Song, Xin, and John Reif. "Nucleic Acid Databases and Molecular-Scale Computing." ACS Nano 13, no. 6 (May 22, 2019): 6256–68. http://dx.doi.org/10.1021/acsnano.9b02562.
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Rigden, Daniel J., and Xosé M. Fernández. "The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection." Nucleic Acids Research 51, no. D1 (January 6, 2023): D1—D8. http://dx.doi.org/10.1093/nar/gkac1186.
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Abstract The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging across biology and related fields. There are 90 papers reporting on new databases and 82 updates from resources previously published in the Issue. Six more papers are updates from databases most recently published elsewhere. Major nucleic acid databases reporting updates include Genbank, ENA, ChIPBase, JASPAR, mirDIP and the Issue's first Breakthrough Article, NACDDB for Circular Dichroism data. Updates from BMRB and RCSB cover experimental protein structural data while AlphaFold 2 computational structure predictions feature widely. STRING and REBASE are stand-out updates in the signalling and enzymes section. Immunology-related databases include CEDAR, the second Breakthrough Article, for cancer epitopes and receptors alongside returning IPD-IMGT/HLA and the new PGG.MHC. Genomics-related resources include Ensembl, GWAS Central and UCSC Genome Browser. Major returning databases for drugs and their targets include Open Targets, DrugCentral, CTD and Pubchem. The EMPIAR image archive appears in the Issue for the first time. 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 updated, revisiting 463 entries, adding 92 new resources and eliminating 96 discontinued URLs so bringing the current total to 1764 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
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Rigden, Daniel J., and Xosé M. Fernández. "The 2021 Nucleic Acids Research database issue and the online molecular biology database collection." Nucleic Acids Research 49, no. D1 (December 23, 2020): D1—D9. http://dx.doi.org/10.1093/nar/gkaa1216.
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Abstract 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/.
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Rigden, Daniel J., and Xosé M. Fernández. "The 27th annual Nucleic Acids Research database issue and molecular biology database collection." Nucleic Acids Research 48, no. D1 (December 22, 2019): D1—D8. http://dx.doi.org/10.1093/nar/gkz1161.
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Abstract The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 papers reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten papers are updates on databases most recently published elsewhere. This issue contains three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools. Major returning nucleic acid databases include miRDB and miRTarBase. Databases for protein sequence analysis include CDD, DisProt and ELM, alongside no fewer than four newcomers covering proteins involved in liquid–liquid phase separation. In metabolism and signaling, Pathway Commons, Reactome and Metabolights all contribute papers. PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser. Immune-related proteins are covered by updates from IPD-IMGT/HLA and AFND, as well as newcomers VDJbase and OGRDB. Drug design is catered for by updates from the IUPHAR/BPS Guide to Pharmacology and the Therapeutic Target Database. 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 revised, updating 305 entries, adding 65 new resources and eliminating 125 discontinued URLs; so bringing the current total to 1637 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
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Rigden, Daniel J., and Xosé M. Fernández. "The 2022 Nucleic Acids Research database issue and the online molecular biology database collection." Nucleic Acids Research 50, no. D1 (December 27, 2021): D1—D10. http://dx.doi.org/10.1093/nar/gkab1195.
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Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.
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Gans, J. D., and M. Wolinsky. "Improved assay-dependent searching of nucleic acid sequence databases." Nucleic Acids Research 36, no. 12 (May 23, 2008): e74-e74. http://dx.doi.org/10.1093/nar/gkn301.
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Sarai, Akinori, M. Michael Gromiha, Jianghong An, Ponraj Prabakaran, Samuel Selvaraj, Hidetoshi Kono, Motohisa Oobatake, and Hatsuho Uedaira. "Thermodynamic databases for proteins and protein-nucleic acid interactions." Biopolymers 61, no. 2 (2001): 121–26. http://dx.doi.org/10.1002/1097-0282(2002)61:2<121::aid-bip10077>3.0.co;2-1.
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Bigot, Thomas, Sarah Temmam, Philippe Pérot, and Marc Eloit. "RVDB-prot, a reference viral protein database and its HMM profiles." F1000Research 8 (April 23, 2019): 530. http://dx.doi.org/10.12688/f1000research.18776.1.
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We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.
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Bigot, Thomas, Sarah Temmam, Philippe Pérot, and Marc Eloit. "RVDB-prot, a reference viral protein database and its HMM profiles." F1000Research 8 (September 7, 2020): 530. http://dx.doi.org/10.12688/f1000research.18776.2.
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We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.
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Sayers, Eric W., Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Ryan Connor, et al. "Database resources of the national center for biotechnology information." Nucleic Acids Research 50, no. D1 (December 1, 2021): D20—D26. http://dx.doi.org/10.1093/nar/gkab1112.
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Abstract The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.
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Coates, David. "Mining proteases in the genome databases." Essays in Biochemistry 38 (October 1, 2002): 185–96. http://dx.doi.org/10.1042/bse0380185.
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Protease data mining can take advantage both of the many specialist, Web-available databases that cover the genetic, protein and nucleic acid sequence information that is specific to a variety of organisms, and of a flexible, but defined, classification system. However, precomputed data, such as gene predictions, should be used with care. Unless there is definitive supporting information, ideally sequencing of a cDNA to show that the predictions are accurate, followed by expression and biochemical characterization of the predicted protein, the predicted gene and its product remains a possibility, rather than a certainty.
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Andrews-Pfannkoch, Cynthia, Douglas W. Fadrosh, Joyce Thorpe, and Shannon J. Williamson. "Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages." Applied and Environmental Microbiology 76, no. 15 (June 11, 2010): 5039–45. http://dx.doi.org/10.1128/aem.00204-10.
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ABSTRACT Metagenomics can be used to determine the diversity of complex, often unculturable, viral communities with various nucleic acid compositions. Here, we report the use of hydroxyapatite chromatography to efficiently fractionate double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), dsRNA, and ssRNA genomes from known bacteriophages. Linker-amplified shotgun libraries were constructed to generate sequencing reads from each hydroxyapatite fraction. Greater than 90% of the reads displayed significant similarity to the expected genomes at the nucleotide level. These methods were applied to marine viruses collected from the Chesapeake Bay and the Dry Tortugas National Park. Isolated nucleic acids were fractionated using hydroxyapatite chromatography followed by linker-amplified shotgun library construction and sequencing. Taxonomic analysis demonstrated that the majority of environmental sequences, regardless of their source nucleic acid, were most similar to dsDNA viruses, reflecting the bias of viral metagenomic sequence databases.
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Kumar, M. D. S. "ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions." Nucleic Acids Research 34, no. 90001 (January 1, 2006): D204—D206. http://dx.doi.org/10.1093/nar/gkj103.
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Wang, Yixuan. "Loop-mediated Iso-thermal amplification (LAMP) used for COVID-19 detection." Theoretical and Natural Science 8, no. 1 (November 13, 2023): 96–102. http://dx.doi.org/10.54254/2753-8818/8/20240365.
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Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification technique, which can be efficiently amplified at constant temperature by using a Bst DNA polymerase with high chain replacement activity. Compared with traditional nucleic acid amplification technology, this technique has the advantages of high sensitivity, strong specificity, simple operation and low detection cost. In the outbreak of COVID-19 in recent years, LAMP technology has been successfully used to develop rapid domestic COVID-19 nucleic acid detection kits with the above advantages, which can achieve rapid detection of COVID-19 in only 20min, greatly improving the convenience and immediacy of nucleic acid detection. In this paper, the principle and development of LAMP technology were summarized by using databases such as NCBI PubMed, Web of Science, CNKI, etc., focusing on the application of LAMP technology in novel coronavirus detection, and the future development direction of LAMP technology was analyzed by describing the latest LAMP technology.
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Cantalupo, Paul G., Joshua P. Katz, and James M. Pipas. "HeLa Nucleic Acid Contamination in The Cancer Genome Atlas Leads to the Misidentification of Human Papillomavirus 18." Journal of Virology 89, no. 8 (January 28, 2015): 4051–57. http://dx.doi.org/10.1128/jvi.03365-14.
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ABSTRACTWe searched The Cancer Genome Atlas (TCGA) database for viruses by comparing non-human reads present in transcriptome sequencing (RNA-Seq) and whole-exome sequencing (WXS) data to viral sequence databases. Human papillomavirus 18 (HPV18) is an etiologic agent of cervical cancer, and as expected, we found robust expression of HPV18 genes in cervical cancer samples. In agreement with previous studies, we also found HPV18 transcripts in non-cervical cancer samples, including those from the colon, rectum, and normal kidney. However, in each of these cases, HPV18 gene expression was low, and single-nucleotide variants and positions of genomic alignments matched the integrated portion of HPV18 present in HeLa cells. Chimeric reads that match a known virus-cell junction of HPV18 integrated in HeLa cells were also present in some samples. We hypothesize that HPV18 sequences in these non-cervical samples are due to nucleic acid contamination from HeLa cells. This finding highlights the problems that contamination presents in computational virus detection pipelines.IMPORTANCEViruses associated with cancer can be detected by searching tumor sequence databases. Several studies involving searches of the TCGA database have reported the presence of HPV18, a known cause of cervical cancer, in a small number of additional cancers, including those of the rectum, kidney, and colon. We have determined that the sequences related to HPV18 in non-cervical samples are due to nucleic acid contamination from HeLa cells. To our knowledge, this is the first report of the misidentification of viruses in next-generation sequencing data of tumors due to contamination with a cancer cell line. These results raise awareness of the difficulty of accurately identifying viruses in human sequence databases.
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Chauhan, Veeren M., Mohamed M. Elsutohy, C. Patrick McClure, William L. Irving, Neil Roddis, and Jonathan W. Aylott. "Gold–Oligonucleotide Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences." Biosensors 11, no. 7 (July 14, 2021): 238. http://dx.doi.org/10.3390/bios11070238.
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Enteroviruses are ubiquitous mammalian pathogens that can produce mild to life-threatening disease. We developed a multimodal, rapid, accurate and economical point-of-care biosensor that can detect nucleic acid sequences conserved amongst 96% of all known enteroviruses. The biosensor harnesses the physicochemical properties of gold nanoparticles and oligonucleotides to provide colourimetric, spectroscopic and lateral flow-based identification of an exclusive enteroviral nucleic acid sequence (23 bases), which was identified through in silico screening. Oligonucleotides were designed to demonstrate specific complementarity towards the target enteroviral nucleic acid to produce aggregated gold–oligonucleotide nanoconstructs. The conserved target enteroviral nucleic acid sequence (≥1 × 10−7 M, ≥1.4 × 10−14 g/mL) initiates gold–oligonucleotide nanoconstruct disaggregation and a signal transduction mechanism, producing a colourimetric and spectroscopic blueshift (544 nm (purple) > 524 nm (red)). Furthermore, lateral-flow assays that utilise gold–oligonucleotide nanoconstructs were unaffected by contaminating human genomic DNA, demonstrated rapid detection of conserved target enteroviral nucleic acid sequence (<60 s), and could be interpreted with a bespoke software and hardware electronic interface. We anticipate that our methodology will translate in silico screening of nucleic acid databases to a tangible enteroviral desktop detector, which could be readily translated to related organisms. This will pave the way forward in the clinical evaluation of disease and complement existing strategies to overcome antimicrobial resistance.
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Singh, Kuljit, and Ipsita Roy. "Nucleic Acid Therapeutics in Huntington’s Disease." Recent Patents on Biotechnology 13, no. 3 (August 6, 2019): 187–206. http://dx.doi.org/10.2174/1872208313666190208163714.
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Background: Protein misfolding is a critical factor in the progression of a large number of neurodegenerative diseases. The incorrectly folded protein is prone to aggregation, leading to aberrant interaction with other cellular proteins, elevated oxidative stress, impaired cellular machinery, finally resulting in cell death. Due to its monogenic origin, Huntington’s disease (HD) is a poster child of protein misfolding neurodegenerative disorders. The presence of neuronal inclusions of mutant huntingtin N-terminal fragments, mainly in the cortex and striatum, is a neuropathological hallmark of HD. Inhibition of protein misfolding and aggregation has been attempted using a variety of conventional protein stabilizers. Methods: This review describes how, in recent times, nucleic acid therapeutics has emerged as a selective tool to downregulate the aberrant transcript and reduce expression of mutant huntingtin, thereby alleviating protein aggregation. Different strategies of use of nucleic acids, including antisense oligonucleotides, short inhibitory RNA sequences and aptamers have been discussed. The following patent databases were consulted: European Patent Office (EPO), the United States Patent and Trademark Office (USPTO), Patent scope Search International and National Patent Collections (WIPO) and Google Patents. Results: Tools such as RNA interference (RNAi) and antisense oligonucleotides (ASOs) are potential therapeutic agents which target the post-transcriptional step, accelerating mRNA degradation and inhibiting the production of the mutant protein. These nucleic acid sequences not only target the elongated CAG triplet repeat translating to an expanded polyglutamine tract in the mutant protein, but have also been used to target single nucleotide polymorphisms associated with the mutant allele. The therapeutic sequences have been investigated in a number of cells and animal models of HD. One antisense sequence, with desirable safety properties, has recently shown downregulation of huntingtin protein in a limited clinical trial. RNA aptamers have also shown promising results in inhibiting protein aggregation in a yeast model of HD. Novel drug delivery techniques have been employed to overcome the blood brain barrier for the use of these therapeutic sequences. Conclusion: The selectivity and specificity imparted by nucleic acids, along with novel delivery techniques, make them hopeful candidates for the development of a curative strategy for HD.
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Bryś, M. "Some useful hosting centers and databases for molecular biology on the World Wide Web." Acta Biochimica Polonica 43, no. 4 (December 31, 1996): 743–51. http://dx.doi.org/10.18388/abp.1996_4472.
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This article describes the information contained within World Wide Web of potential uses for molecular biologists. The aim is to provide a basic description of the server provided services of bioinformatics, major program coordinator activities, and current contents of genome nucleic acid and protein databases.
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Novére, Nicolas Le, and Jean-Pierre Changeux. "The Ligand Gated Ion Channel database: an example of a sequence database in neuroscience." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 356, no. 1412 (August 29, 2001): 1121–30. http://dx.doi.org/10.1098/rstb.2001.0903.
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Multiple comparisons of receptor sequences, or receptor subunit sequences, has proved to be an invaluable tool in modern pharmacological investigations. Although of outstanding importance, general sequence databases suffer from several imperfections due to their size and their non–specificity. Room therefore exists for expert–maintained databases of restricted focus, where knowledge of the research field helps to filter the huge amount of data generated. Accordingly, neuroscientists have designed databases covering several types of proteins, in particular receptors for neurotransmitters. Ligand–gated ion channels are oligomeric transmembrane proteins involved in the fast response to neurotransmitters. All these receptors are formed by the assembly of homologous subunits, and an unexpected wealth of genes coding for these subunits has been revealed during the last two decades. The Ligand Gated Ion Channel database (LGICdb) has been developed to handle this growing body of information. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences.
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Siddiqui, M., Maulik Badmalia, and Trushar Patel. "Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins." International Journal of Molecular Sciences 22, no. 5 (March 5, 2021): 2647. http://dx.doi.org/10.3390/ijms22052647.
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Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.
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Chantre-Justino, Mariana, Lucas Delmonico, Claudia Lage, Maria G. C. Carvalho, Maria Helena F. Ornellas, and Gilda Alves. "Tracking the history of circulating nucleic acids for cancer research in Brazil: A systematic review." Brazilian Journal of Health and Biomedical Sciences 20, no. 2 (February 25, 2022): 135–43. http://dx.doi.org/10.12957/bjhbs.2021.63966.
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Introduction: Circulating nucleic acids can be obtainedby minimally invasive procedures based on liquid biopsy,which has emerged as a promising area of investigation forscreening and monitoring cancer treatment. Currently, testsbased on circulating nucleic acid analysis, specifically cellfreeDNA (cfDNA), are commercially available for diagnosticand prognostic investigation of a number of neoplasms. Objective:To describe the research on circulating nucleic acidmarkers for cancer prospecting in Brazil, since this area hasadvanced rapidly in recent years. Methods: In this systematicreview, we surveyed Brazilian publications in cancer researchfocused on cfDNA and cfRNA present in different fluids. BothMEDLINE-PUBMED and EMBASE databases were inspectedusing terms such as “circulating nucleic acids”, “cancer”, and“Brazil”. Results: The search returned 326 articles, in which28 Brazilian translational studies were eligible. Differentmethodologies were reported for different types of cancer,in which cfDNA from plasma was the most investigatedbiological material. Molecular investigations included quantification,somatic mutation, RNA expression, genotyping,microsatellites, blood protein interaction, and methylation.Discrepancies in the regional distribution of the studies werealso observed. Conclusion: Studies on circulating nucleic acidmarkers have advanced significantly in the oncology field,but many others are needed to better address the clinicalpractice in Brazil.
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Pruess, Manuela, and Rolf Apweiler. "Bioinformatics Resources for In Silico Proteome Analysis." Journal of Biomedicine and Biotechnology 2003, no. 4 (2003): 231–36. http://dx.doi.org/10.1155/s1110724303209219.
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In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species—mainly the human—have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, characterisation, and classification of protein sequences. Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling, respectively, comprehensive databases like the proteome analysis database benefit from the information stored in different databases and make use of different protein analysis tools to provide computational analysis of whole proteomes.
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Tung, Chang-Shung, and Christian Burks. "Characterization of the distribution of potential short restriction fragments in nucleic acid sequence databases." FEBS Letters 205, no. 2 (September 15, 1986): 299–302. http://dx.doi.org/10.1016/0014-5793(86)80916-4.
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Seyoum Tola, Fikadu. "The concept of folic acid supplementation and its role in prevention of neural tube defect among pregnant women: PRISMA." Medicine 103, no. 19 (May 10, 2024): e38154. http://dx.doi.org/10.1097/md.0000000000038154.
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Folic acid is the synthetic form of vitamin B9, found in supplements and fortified foods, while folate occurs naturally in foods. Folic acid and its derivatives are extremely important in the synthesis of nucleic acids (DNA and ribose nucleic acid [RNA]) and different proteins. It acts as a coenzyme for the transfer of 1 carbon in the biosynthesis of purine, pyrimidine, and amino acids. Folic acid is critically important in rapidly proliferating tissues, including fetus and trophoblastic tissue to prevent neural tube defect (NTD). The main objective of this review is to identify the role of folic acid to prevent NTD among pregnancy mothers. Electronic databases including Web of Science, Google Scholar, MEDLINE, Scopus, and Cochrane library used to systematically search without limitation of publication date and status. In pregnancy, the first trimester is a significant time for neural tube closure. Decreased blood folic acid levels inhibit DNA replication, repair, RNA synthesis, histone and DNA methylation, methionine production, and homocysteine remethylation reactions that cause NTDs in pregnancy. Therefore, folic acid supplementation is critically important for childbearing mothers before conception and in the first trimester pregnancy. As a result, women are recommended to take 400 microgram FA/day from preconception until the end of the first trimester to prevent NTD-affected pregnancies. This allows the developing neural tissue to acquire critical mass and provides the preferred rostrocaudal orientation so that these divisions contribute to the elongation of the developing neural tube in embryos.
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MILED, ZINA BEN, YUE W. WEBSTER, YANG LIU, and NIANHUA LI. "AN ONTOLOGY FOR SEMANTIC INTEGRATION OF LIFE SCIENCE WEB DATABASES." International Journal of Cooperative Information Systems 12, no. 02 (June 2003): 275–94. http://dx.doi.org/10.1142/s0218843003000747.
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The incompatibilities among complex data formats and various schema used by biological databases that house these data are becoming a bottleneck in biological research. For example, biological data format varies from simple words (e.g. gene name), numbers (e.g. molecular weight) to sequence strings (e.g. nucleic acid sequence), to even more complex data formats such as taxonomy trees. Some information is embedded in narrative text, such as expert comments and publications. Some other information is expressed as graphs or images (e.g. pathways networks). The confederation of heterogeneous web databases has become a crucial issue in today's biological research. In other words, interoperability has to be archieved among the biological web databases and the heterogeneity of the web databases has to be resolved. This paper presents a biological ontology, BAO, and discusses its advantages in supporting the semantic integration of biological web databases are discussed.
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Gouy, M., C. Gautier, M. Attimonelli, C. Lanave, and G. di Paola. "ACNUC – a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage." Bioinformatics 1, no. 3 (1985): 167–72. http://dx.doi.org/10.1093/bioinformatics/1.3.167.
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Ahmad Faris, Asma Nadia, Mohamad Ahmad Najib, Muhammad Najmi Mohd Nazri, Amir Syahir Amir Hamzah, Ismail Aziah, Nik Yusnoraini Yusof, Rohimah Mohamud, Irneza Ismail, and Fatin Hamimi Mustafa. "Colorimetric Approach for Nucleic Acid Salmonella spp. Detection: A Systematic Review." International Journal of Environmental Research and Public Health 19, no. 17 (August 25, 2022): 10570. http://dx.doi.org/10.3390/ijerph191710570.
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Water- and food-related health issues have received a lot of attention recently because food-poisoning bacteria, in particular, are becoming serious threats to human health. Currently, techniques used to detect these bacteria are time-consuming and laborious. To overcome these challenges, the colorimetric strategy is attractive because it provides simple, rapid and accurate sensing for the detection of Salmonella spp. bacteria. The aim of this study is to review the progress regarding the colorimetric method of nucleic acid for Salmonella detection. A literature search was conducted using three databases (PubMed, Scopus and ScienceDirect). Of the 88 studies identified in our search, 15 were included for further analysis. Salmonella bacteria from different species, such as S. Typhimurium, S. Enteritidis, S. Typhi and S. Paratyphi A, were identified using the colorimetric method. The limit of detection (LoD) was evaluated in two types of concentrations, which were colony-forming unit (CFU) and CFU per mL. The majority of the studies used spiked samples (53%) rather than real samples (33%) to determine the LoDs. More research is needed to assess the sensitivity and specificity of colorimetric nucleic acid in bacterial detection, as well as its potential use in routine diagnosis.
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Zhang, Jian, Zhiqiang Ma, and Lukasz Kurgan. "Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains." Briefings in Bioinformatics 20, no. 4 (December 15, 2017): 1250–68. http://dx.doi.org/10.1093/bib/bbx168.
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Abstract Proteins interact with a variety of molecules including proteins and nucleic acids. We review a comprehensive collection of over 50 studies that analyze and/or predict these interactions. While majority of these studies address either solely protein–DNA or protein–RNA binding, only a few have a wider scope that covers both protein–protein and protein–nucleic acid binding. Our analysis reveals that binding residues are typically characterized with three hallmarks: relative solvent accessibility (RSA), evolutionary conservation and propensity of amino acids (AAs) for binding. Motivated by drawbacks of the prior studies, we perform a large-scale analysis to quantify and contrast the three hallmarks for residues that bind DNA-, RNA-, protein- and (for the first time) multi-ligand-binding residues that interact with DNA and proteins, and with RNA and proteins. Results generated on a well-annotated data set of over 23 000 proteins show that conservation of binding residues is higher for nucleic acid- than protein-binding residues. Multi-ligand-binding residues are more conserved and have higher RSA than single-ligand-binding residues. We empirically show that each hallmark discriminates between binding and nonbinding residues, even predicted RSA, and that combining them improves discriminatory power for each of the five types of interactions. Linear scoring functions that combine these hallmarks offer good predictive performance of residue-level propensity for binding and provide intuitive interpretation of predictions. Better understanding of these residue-level interactions will facilitate development of methods that accurately predict binding in the exponentially growing databases of protein sequences.
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Sayers, Eric W., Jeff Beck, J. Rodney Brister, Evan E. Bolton, Kathi Canese, Donald C. Comeau, Kathryn Funk, et al. "Database resources of the National Center for Biotechnology Information." Nucleic Acids Research 48, no. D1 (October 11, 2019): D9—D16. http://dx.doi.org/10.1093/nar/gkz899.
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Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
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Sayers, Eric W., Jeffrey Beck, Evan E. Bolton, Devon Bourexis, James R. Brister, Kathi Canese, Donald C. Comeau, et al. "Database resources of the National Center for Biotechnology Information." Nucleic Acids Research 49, no. D1 (October 23, 2020): D10—D17. http://dx.doi.org/10.1093/nar/gkaa892.
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Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 34 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface and NCBI datasets. Additional resources that were updated in the past year include PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.
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Moll, Keran, Shayan Hobbi, Cindy Ke Zhou, Kathryn Fingar, Timothy Burrell, Veronica Hernandez-Medina, Joyce Obidi, et al. "Assessment of performance characteristics of COVID-19 ICD-10-CM diagnosis code U07.1 using SARS-CoV-2 nucleic acid amplification test results." PLOS ONE 17, no. 8 (August 18, 2022): e0273196. http://dx.doi.org/10.1371/journal.pone.0273196.
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The Food and Drug Administration’s Biologics Effectiveness and Safety Initiative conducts active surveillance to protect public health during the coronavirus disease 2019 (COVID-19) pandemic. This study evaluated performance of International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) diagnosis code U07.1 in identifying COVID-19 cases in claims compared with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid amplification test results in linked electronic health records (EHRs). Care episodes in three populations were defined using COVID-19-related diagnoses (population 1), SARS-CoV-2 nucleic acid amplification test procedures (population 2), and all-cause hospitalizations (population 3) in two linked claims-EHR databases: IBM® MarketScan® Explorys® Claims-EMR Data Set (commercial) and OneFlorida Data Trust linked Medicaid-EHR. Positive and negative predictive values were calculated. Respectively, populations 1, 2, and 3 included 26,686, 26,095, and 2,564 episodes (commercial) and 29,117, 23,412, and 9,629 episodes (Florida Medicaid). The positive predictive value was >80% and the negative predictive value was >95% in each population, with the highest positive predictive value in population 3 (commercial: 91.9%; Medicaid: 93.1%). Findings did not vary substantially by patient age. Positive predictive values in populations 1 and 2 fluctuated during April–June 2020. They then stabilized in the commercial but not the Medicaid population. Negative predictive values were consistent over time in all populations and databases. Our findings indicate that U07.1 has high performance in identifying COVID-19 cases and noncases in claims databases. Performance may vary across populations and periods.
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Blum, Matthias, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, et al. "The InterPro protein families and domains database: 20 years on." Nucleic Acids Research 49, no. D1 (November 6, 2020): D344—D354. http://dx.doi.org/10.1093/nar/gkaa977.
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Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.
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Stobbe, A. H., W. L. Schneider, P. R. Hoyt, and U. Melcher. "Screening Metagenomic Data for Viruses Using the E-Probe Diagnostic Nucleic Acid Assay." Phytopathology® 104, no. 10 (October 2014): 1125–29. http://dx.doi.org/10.1094/phyto-11-13-0310-r.
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Next generation sequencing (NGS) is not used commonly in diagnostics, in part due to the large amount of time and computational power needed to identify the taxonomic origin of each sequence in a NGS data set. By using the unassembled NGS data sets as the target for searches, pathogen-specific sequences, termed e-probes, could be used as queries to enable detection of specific viruses or organisms in plant sample metagenomes. This method, designated e-probe diagnostic nucleic acid assay, first tested with mock sequence databases, was tested with NGS data sets generated from plants infected with a DNA (Bean golden yellow mosaic virus, BGYMV) or an RNA (Plum pox virus, PPV) virus. In addition, the ability to detect and differentiate among strains of a single virus species, PPV, was examined by using probe sets that were specific to strains. The use of probe sets for multiple viruses determined that one sample was dually infected with BGYMV and Bean golden mosaic virus.
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Du, Yan, Tongtong Wang, Bo Li, Fang Pang, Xuanguo Zhang, and Li Xi. "Lopinavir/Ritonavir in the Treatment of COVID-19: A Systematic Review and Meta-Analysis." Proceedings of Anticancer Research 5, no. 5 (September 24, 2021): 19–25. http://dx.doi.org/10.26689/par.v5i5.2502.
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Objective: To systematically evaluate the efficacy and safety of lopinavir/ritonavir (LPV/r) in the treatment of COVID-19. Methods: PubMed, Embase, Ovid, CNKI, CBM, Wanfang, and VIP databases were searched to obtain the clinical studies of LPV/r in the treatment of COVID-19 from December 2019 to July 2020. The literatures were screened according to the inclusion and exclusion criteria. Their qualities were evaluated according to the Newcastle-Ottawa Scale (NOS) and RevMan 5.3 software was used for meta-analysis. Results: A total of 688 patients were included in five studies, involving China and France. Compared with patients in the control group, who was only treated with routine treatment, there were no significant differences of the 7-day nucleic acid negative conversion rate and 14-day nucleic acid negative conversion rate in the treatment group. However, the use of LPV/r increased the incidence of adverse reactions in the treatment group compared to the control group. Conclusion: There is no available evidence to support the use of Lopinavir/ritonavir in the treatment of COVID-19.
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Areo, Oluwatoyin, Pratik U. Joshi, Mark Obrenovich, Moncef Tayahi, and Caryn L. Heldt. "Single-Particle Characterization of SARS-CoV-2 Isoelectric Point and Comparison to Variants of Interest." Microorganisms 9, no. 8 (July 28, 2021): 1606. http://dx.doi.org/10.3390/microorganisms9081606.
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SARS-CoV-2, the cause of COVID-19, is a new, highly pathogenic coronavirus, which is the third coronavirus to emerge in the past 2 decades and the first to become a global pandemic. The virus has demonstrated itself to be extremely transmissible and deadly. Recent data suggest that a targeted approach is key to mitigating infectivity. Due to the proliferation of cataloged protein and nucleic acid sequences in databases, the function of the nucleic acid, and genetic encoded proteins, we make predictions by simply aligning sequences and exploring their homology. Thus, similar amino acid sequences in a protein usually confer similar biochemical function, even from distal or unrelated organisms. To understand viral transmission and adhesion, it is key to elucidate the structural, surface, and functional properties of each viral protein. This is typically first modeled in highly pathogenic species by exploring folding, hydrophobicity, and isoelectric point (IEP). Recent evidence from viral RNA sequence modeling and protein crystals have been inadequate, which prevent full understanding of the IEP and other viral properties of SARS-CoV-2. We have thus experimentally determined the IEP of SARS-CoV-2. Our findings suggest that for enveloped viruses, such as SARS-CoV-2, estimates of IEP by the amino acid sequence alone may be unreliable. We compared the experimental IEP of SARS-CoV-2 to variants of interest (VOIs) using their amino acid sequence, thus providing a qualitative comparison of the IEP of VOIs.
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Drees, Alissa, Tung Lam Trinh, and Markus Fischer. "The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers." Pharmaceuticals 16, no. 3 (March 18, 2023): 457. http://dx.doi.org/10.3390/ph16030457.
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Aptamers offer several advantages over antibodies. However, to ensure high affinity and specificity, a better understanding of the interactions between the nucleic-acid-based aptamers and their targets is mandatory. Therefore, we investigated the influence of two physical properties of proteins—molecular mass and charge—on the affinity of nucleic-acid-based aptamers. For this purpose, first, the affinity of two random oligonucleotides towards twelve proteins was determined. No binding was observed for proteins with a negative net charge towards the two oligonucleotides, while up to nanomolar affinity was determined for positively charged proteins with a high pI value. Second, a literature analysis comprising 369 aptamer–peptide/protein pairs was performed. The dataset included 296 different target peptides and proteins and is thus currently one of the largest databases for aptamers for proteins and peptides. The targets considered covered isoelectric points of 4.1–11.8 and a molecular weight range of 0.7–330 kDa, while the dissociation constants ranged from 50 fM to 29.5 µM. This also revealed a significant inverse correlation between the protein’s isoelectric point and the affinity of aptamers. In contrast, no trend was observed between the affinity and the molecular weight of the target protein with either approach.
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Peryea, Tyler, Noel Southall, Mitch Miller, Daniel Katzel, Niko Anderson, Jorge Neyra, Sarah Stemann, et al. "Global Substance Registration System: consistent scientific descriptions for substances related to health." Nucleic Acids Research 49, no. D1 (November 2, 2020): D1179—D1185. http://dx.doi.org/10.1093/nar/gkaa962.
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Abstract The US Food and Drug Administration (FDA) and the National Center for Advancing Translational Sciences (NCATS) have collaborated to publish rigorous scientific descriptions of substances relevant to regulated products. The FDA has adopted the global ISO 11238 data standard for the identification of substances in medicinal products and has populated a database to organize the agency's regulatory submissions and marketed products data. NCATS has worked with FDA to develop the Global Substance Registration System (GSRS) and produce a non-proprietary version of the database for public benefit. In 2019, more than half of all new drugs in clinical development were proteins, nucleic acid therapeutics, polymer products, structurally diverse natural products or cellular therapies. While multiple databases of small molecule chemical structures are available, this resource is unique in its application of regulatory standards for the identification of medicinal substances and its robust support for other substances in addition to small molecules. This public, manually curated dataset provides unique ingredient identifiers (UNIIs) and detailed descriptions for over 100 000 substances that are particularly relevant to medicine and translational research. The dataset can be accessed and queried at https://gsrs.ncats.nih.gov/app/substances.
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Tessaro, Leticia, Adriano Aquino, Paloma de Almeida Rodrigues, Nirav Joshi, Rafaela Gomes Ferrari, and Carlos Adam Conte-Junior. "Nucleic Acid-Based Nanobiosensor (NAB) Used for Salmonella Detection in Foods: A Systematic Review." Nanomaterials 12, no. 5 (February 28, 2022): 821. http://dx.doi.org/10.3390/nano12050821.
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Salmonella bacteria is a foodborne pathogen found mainly in food products causing severe symptoms in the individual, such as diarrhea, fever, and abdominal cramps after consuming the infected food, which can be fatal in some severe cases. Rapid and selective methods to detect Salmonella bacteria can prevent outbreaks when ingesting contaminated food. Nanobiosensors are a highly sensitive, simple, faster, and lower cost method for the rapid detection of Salmonella, an alternative to conventional enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) techniques. This study systematically searched and analyzed literature data related to nucleic acid-based nanobiosensors (NABs) with nanomaterials to detect Salmonella in food, retrieved from three databases, published between 2010 and 2021. We extracted data and critically analyzed the effect of nanomaterial functionalized with aptamer or DNA at the limit of detection (LOD). Among the nanomaterials, gold nanoparticles (AuNPs) were the most used nanomaterial in studies due to their unique optical properties of the metal, followed by magnetic nanoparticles (MNPs) of Fe3O4, copper nanoparticles (CuNPs), and also hybrid nanomaterials multiwalled carbon nanotubes (c-MWCNT/AuNP), QD/UCNP-MB (quantum dotes upconverting nanoparticle of magnetic beads), and cadmium telluride quantum dots (CdTe QDs@MNPs) showed excellent LOD values. The transducers used for detection also varied from electrochemical, fluorescent, surface-enhanced Raman spectroscopy (SERS), RAMAN spectroscopy, and mainly colorimetric due to the possibility of visualizing the detection result with the naked eye. Furthermore, we show the magnetic separation system capable of detecting the target amplification of the genetic material. Finally, we present perspectives, future research, and opportunities to use point-of-care (POC) diagnostic devices as a faster and lower cost approach for detecting Salmonella in food as they prove to be viable for resource-constrained environments such as field-based or economically limited conditions.
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Bruce K Kowiatek. "Did transfer RNA evolve from a ribozyme? An in-silico study." International Journal of Frontiers in Science and Technology Research 2, no. 2 (June 30, 2022): 024–30. http://dx.doi.org/10.53294/ijfstr.2022.2.2.0037.
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Transfer RNA (tRNA) is widely believed to be one of the oldest, if not the oldest nucleic acid on Earth. Concurrently, ribozymes, RNA-only catalysts that perform many of the same functions as present-day protein enzymes, are also thought to be just as ancient. While the position has been posited that tRNA, nature’s chief aminoacylator of amino acids with the assistance of aminoacyl-tRNA synthetase (aaRS) protein enzymes, evolved from a self-aminoacylating ribozyme, no studies have been performed, to the best of this author’s knowledge, searching for nucleotide sequence correlation between the two; such correlation would indicate the conservation of part or all of such a ribozyme in modern-day tRNA. To that end, an in-silico study utilizing several databases was performed to search for a high percentage of highly conserved nucleotide sequences in archaea, believed to be the most ancient of organisms, with very successful results and their implications discussed here.
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Zhytnikova, M. Yu, and A. V. Shestopalova. "ProtNA-ASA data base: new version including information about electrostatic potential of DNA minor groove." 48, no. 48 (January 30, 2023): 18–24. http://dx.doi.org/10.26565/2075-3810-2022-48-02.
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Background: In the past decades, the rapid development of molecular biology has led to a generation of an unprecedented amount of biological data obtained by the scientific community. Therefore, there is a significant and unmet need to store, process, and make sense of such a vast amount of data. There are currently available a number of databases, that cover different fields of molecular biology. Objectives: In this paper, we describe Protein-Nucleic Acid Structural Database with Information on Accessible Surface Area, ProtNA-ASA, http://www.ire.kharkov.ua/ProtNA-ASA/index.php. The main aim of ProtNA-ASA is to provide quick and convenient access to structural information about DNA and protein-DNA complexes, that can be used for comprehensive study of protein-DNA recognition. Materials and Methods: ProtNA-ASA database comprise information based on X-ray or NMR structures derived from Nucleic Acids Data Bank: 973 structures of protein-DNA complexes, 129 structures of naked А- and 403 of B-DNA ones; following structural parameters for each structure: conformational DNA parameters calculated with the 3DNA/CompDNA analyzer; DNA accessible surface area calculated using the modified algorithm of Higo and Go; DNA electrostatic potential calculated with DelPhi package. Results: The recent update of ProtNA-ASA includes the electrostatic potential of the DNA minor groove since it plays an essential role in the indirect protein-DNA recognition process. The update also includes an advanced search, which serves to ease the use of the database and contribute to a more accurate structure selection. Advanced search allows finding structures by PDB/NDB ID, citation, length and sequence of a protein or DNA chain, type of structure, method of structure obtaining and resolution. All these queries can be used in different combinations with and/or statements. Conclusion: The combination of structural information and physical characteristics from the ProtNA-ASA database is particularly useful to scientists studying the indirect readout, that based on DNA deformability. The detail analyzes of protein-DNA complexes and mechanisms of protein-DNA recognition is essential for implications in understanding cellular processes, DNA metabolism, transcriptional regulation, and developing therapeutic drugs.
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Yao, Xiao-Yan, Shao-Qi Yu, Na Tian, Fei Wang, Shi-Zhu Li, and Lan-Hua Li. "Nucleic Acid Prevalence of Zoonotic Babesia in Humans, Animals and Questing Ticks, a Systematic Review and Meta-Analysis." Tropical Medicine and Infectious Disease 8, no. 3 (February 22, 2023): 132. http://dx.doi.org/10.3390/tropicalmed8030132.
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Background: Zoonotic Babesia infections are an emerging public health threat globally. The geographical distribution, animal reservoirs and tick vectors vary greatly across Babesia species, and estimations of prevalence reported in works within the literature are also quite different. Better prevalence estimates and identification of moderators are needed to understand the global transmission risk of different zoonotic Babesia species, and to provide crucial background information for the diagnosis, treatment and control of zoonotic babesiosis. Methods: We conducted a systematic review and meta-analysis to determine the global nucleic acid prevalence of different zoonotic Babesia species in humans, animals and ticks. Relevant publications were obtained from several electronic databases and grey literature up to December 2021. Articles were included if they were published in English or Chinese and reported the nucleic acid prevalence of zoonotic Babesia species in humans, animals or ticks. The pooled estimates of prevalence were determined using a random effect model. Heterogeneity was investigated using subgroup analyses and random effect meta-regression models. Results: Of 3205 unique studies, 28 were included by the systematic review of zoonotic Babesia for humans, 79 for animals and 104 for ticks. The results showed overall pooled estimates of nucleic acid prevalence for the following: B. microti—1.93% (0.32–4.69%) in humans; B. microti—7.80% (5.25–10.77%), B. divergens—2.12% (0.73–4.08%) and B. venatorum—1.42% (0.30–3.16%) in animals; and B. microti—2.30% (1.59–3.13%), B. divergens—0.16% (0.05–0.32%), and B. venatorum—0.39% (0.26–0.54%) in questing ticks. The type of population, animal reservoir or tick vector, detecting method and continent were moderators possibly associated with heterogeneity, yet the remaining heterogeneity that was not explained was still substantial (all QE p values < 0.05). Conclusions: B. microti is the most prevalent and widely distributed zoonotic Babesia species globally. The wide range of suitable animal reservoirs and potential transmission vectors and high prevalence in animals and ticks may contribute to the worldwide distribution of B. microti. Other zoonotic Babesia species were relatively less prevalent and were reported in quite limited areas.
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Ghaffari, Maryam, Nima Sanadgol, and Mohammad Abdollahi. "A Systematic Review of Current Progresses in the Nucleic Acid-Based Therapies for Neurodegeneration with Implications for Alzheimer’s Disease." Mini-Reviews in Medicinal Chemistry 20, no. 15 (October 16, 2020): 1499–517. http://dx.doi.org/10.2174/1389557520666200513122357.
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Recently, manipulation of gene expression and switching genes on or off highlight the potential of nucleic acid-based therapies (NA-BTs). Alzheimer’s Disease (AD) is a common devastating neurodegenerative disease (NDs) responsible for 60-80% of all cases of dementia and predicted as a main public health concern among aged populations. The aim of this study was to outline the current research in the field of NA-BTs for the treatment of AD disabilities, including strategies to suppress the memory and learning defects, to promote recovery processes, and to reinforce social relationships in these patients. This review was performed via evaluating PubMed reported studies from January 2010 to November 2019. Also, reference lists were checked to find additional studies. All intermediation or complementarity of animal models, case-control and cohort studies, and controlled trials (CTs) on specific NA-BTs to AD were acceptable, although in vitro studies were excluded due to the considerable diversities and heterogeneities. After removing the duplicates according to preferred reporting items for systematic reviews and meta-analyses (PRISMA) instruction, we merged remaining titles across search databases. There are 48 ongoing studies related to the application of nucleic acids in the treatment and diagnosis of AD where more consideration is given to DNA targeting strategies (18 targets for vectors and aptamers), antisense oligonucleotides (10 targets), micro-RNAs mimics (7 targets), antagomiRs (6 targets), small interferences-RNAs (5 targets), as well as mRNAs (2 targets) respectively. All of these targets are grouped into 4 categories according to their role in molecular pathways where amyloid-β (18 targets), neural survival (11 targets), memory and cognition (8 targets), and tau (3 targets) are more targeted pathways, respectively. With recent successes in the systemic delivery of nucleic acids via intravenous injection; it is worth investing in the production of new-generation medicines. There are still several challenges for NA-BTs including, their delivery to the effective modulators, mass production at low cost, sustaining efficacy and minimizing off‐target effects. Regarding miRNA-based therapies, given the obvious involvement of miRNAs in numerous facets of brain disease, and the many sophisticated techniques for delivery to the brain, miRNA-based therapies will make new hope for the treatment of neurological diseases such as AD.
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Saunders-Hastings, Patrick, Cindy Ke Zhou, Shayan Hobbi, Eva Boyd, Patricia Lloyd, Nader Alawar, Timothy Burrell, et al. "Characterization of COVID-19 Hospitalized Patients in Three United States Electronic Health Record Databases." Pathogens 12, no. 3 (March 1, 2023): 390. http://dx.doi.org/10.3390/pathogens12030390.
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COVID-19 infections have contributed to substantial increases in hospitalizations. This study describes demographics, baseline clinical characteristics and treatments, and clinical outcomes among U.S. patients admitted to hospitals with COVID-19 during the prevaccine phase of the pandemic. A total of 20,446 hospitalized patients with a positive COVID-19 nucleic acid amplification test were identified from three large electronic health record databases during 5 February–30 November 2020 (Academic Health System: n = 4504; Explorys; n = 7492; OneFlorida: n = 8450). Over 90% of patients were ≥30 years of age, with an even distribution between sexes. At least one comorbidity was recorded in 84.6–96.1% of patients; cardiovascular and respiratory conditions (28.8–50.3%) and diabetes (25.6–44.4%) were most common. Anticoagulants were the most frequently reported medications on or up to 28 days after admission (44.5–81.7%). Remdesivir was administered to 14.1–24.6% of patients and increased over time. Patients exhibited higher COVID-19 severity 14 days following admission than the 14 days prior to and on admission. The length of in-patient hospital stay ranged from a median of 4 to 6 days, and over 85% of patients were discharged alive. These results promote understanding of the clinical characteristics and hospital-resource utilization associated with hospitalized COVID-19 over time.
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Irani-Shemirani, Mahnaz. "Biomarkers approach in the diagnosis and prognosis of sepsis: A review." International Journal of Public Health Research 12, no. 02 (September 1, 2022): 1617–24. http://dx.doi.org/10.17576/ijphr.1202.2022.04.
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Introduction Sepsis is a systematic host response to infection accompanied by suppression of immune system and organ failure. Rapid diagnosis of sepsis has prompted researchers to use circulating biomarkers for diagnosis sepsis. Method The PubMed, and Google Scholar databases were searched from 2010 until 2020 using the keyorganis “sepsis”, “biomarker”, “pathophysiology”, “pathogenesis”, and “diagnose” with restriction by language to English. For each individual biomarker the databases were searched again by the biomarker name. Results Although CRP and Procalcitonin are the most common biomarkers in the diagnosis of sepsis, other biomarkers such as pro-inflammatory and anti-inflammatory cytokines and chemokines, monocyte and lymphocyte biomarkers, antibody and nucleic acid biomarkers may help in diagnosis of sepsis. Conclusion The biomarkers verified capability in disease progress, prognosis of disorder, risk stratification, and treatment effect rather than diagnosis at early stage of sepsis. Defining molecular properties in septic patients opens up new means to diagnose and manage sepsis in a shorter time compared to conventional methods currently used at hospitals however further clinical evaluation of biomarkers should be performed. Keywords. Sepsis. Biomarkers. Prognosis. Diagnosis
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NG, E. Y. K., and L. L. TAY. "STUDY OF BLAST DNA MATCHING TOOLKITS." Journal of Mechanics in Medicine and Biology 04, no. 03 (September 2004): 341–59. http://dx.doi.org/10.1142/s0219519404001090.
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The beginning of bioinformatics saw the development of algorithms that enabled the storage of nucleic acid and protein sequences in the form of annotated databases in a manner that would allow researchers to exchange information about gene and protein sequences easily and quickly. Databases are growing extremely fast, hence it is essential to use the current databases, which are easily available on the Web. This tutorial deals with the concept of DNA matching by using BLAST programs such as BLASTN and MEGABLAST to perform similarity sequence search and to evaluate their relative effectiveness. Interpretation of the BLAST results is done. Comparisons between the two algorithms are included based on varying parameters such as word sizes, query sequences length and gap X drop-off values, etc. It is found that as the word size increases, the computation time for both BLASTN and MEGABLAST algorithms decreases. BLASTN is more sensitive than MEGABLAST since it uses a shorter default word size of 11 as compared to MEGABLAST, which uses a default word size of 28. The search strategy offers a tradeoff between speed and sensitivity. As for BLAST 2 Sequences, MEGABLAST could perform better than BLASTN only for large word sizes greater than or equal to 16 and for longer sequences.
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Xu, Yan, Lizhong Ding, Zhongtian Wang, Yanbo Wang, and Liping Sun. "Virtual Screening of Cablin Patchouli Herb as a Treatment for Heat Stress: A Study Based on Network Pharmacology, Molecular Docking, and Experimental Verification." Evidence-Based Complementary and Alternative Medicine 2021 (March 10, 2021): 1–14. http://dx.doi.org/10.1155/2021/8057587.
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Heat-related diseases have long been known to damage the structure and function of essential macromolecules such as proteins, lipids, and nucleic acids, thereby compromising the integrity of cells and tissues and the physiological functions of the entire organism. Heat stress is the physical discomfort caused by overheating the body and is also the initial manifestation of heat-related diseases. Cablin patchouli herb (CPB) has been used in China for two thousand years and has been used to treat heat stress, but to date, no related mechanistic research is available. In this study, KEGG and PPI networks and the TCMSP and GEO databases were used to explore the components of CPB in relation to heat stress: quercetin, genkwanin, irisolidone, 3,23-dihydroxy-12-oleanen-28-oic acid, and quercetin 7-O-β-D-glucoside. The targets identified were EGFR, NCOA1, FOS, HIF1A, NFKBIA, and NCOA2; these proteins were verified by molecular docking and experimental verification. In short, our research represents the first report on the use of the traditional Chinese medicine CPB to treat heat stress and thus has pioneering significance.