Tag: NAR
Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness
Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…
Genomic characteristics of ESBL-producing E. coli in China
Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…
Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data
Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…
A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
Lederberg, J., Cavalli, L. L. & Lederberg, E. M. Sex compatibility in Escherichia Coli. Genetics 37, 720–730 (1952). Article CAS PubMed PubMed Central Google Scholar Elisabeth, G., Günther, M. & Manuel, E. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301 (2003). Article Google Scholar de la…
Survival outcomes and relapses in testicular DLBCL
Introduction Primary testicular lymphoma, which accounts for less than 2% of non-Hodgkin lymphoma (NHL) cases, has similarities to extra-nodal NHL that occurs in immune-privileged sites, such as the eye and central nervous system (CNS).1 Pathologically, 80–90% of primary testicular lymphoma cases demonstrate diffuse large B-cell lymphoma (DLBCL) with non-germinal center/activated…
Genomic characteristics of a multidrug-resistant E. coli
Introduction Escherichia coli, a member of the Enterobacterales family, is a common opportunistic pathogen that can cause various infectious illnesses, including urinary tract infections (UTIs) and other infections acquired in the community.1,2 The presence of carbapenemases in E. coli poses a serious threat to public health. These carbapenemase genes may…
Backcrossing to different parents produced two distinct hybrid species
Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma 12:246. doi.org/10.1186/1471-2105-12-246 Article Google Scholar Anderegg WRL, Flint A, Huang C-Y, Flint L, Berry JA, Davis FW et al. (2015) Tree mortality predicted from drought-induced vascular damage. Nat Geosci 8:367–371 Article CAS Google Scholar …
Environmental Factor – June 2023: Intramural Papers of the Month
IntramuralBy Janelle Weaver and Meklit Daniel Expanding gene sequencing tool use in environmental carcinogen studies A technique called whole exome sequencing (WES) has been successfully applied to rats to study how a fungal toxin may induce liver cancer, according to NIEHS researchers and their collaborators. Aflatoxin B1 (AFB1)…
Transfer learning enables predictions in network biology
Vaswani, A. et al. Attention is all you need. Preprint at doi.org/10.48550/arXiv.1706.03762 (2017). Devlin, J., Chang, M. W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conference North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1…
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article ADS CAS PubMed Google Scholar Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article Google Scholar Darwin, C. The Descent of Man, and Selection…
RPA-CRISPR/Cas12a mediated isothermal amplification for visual detection of Phytophthora sojae
Introduction Phytophthora sojae is among the most destructive pathogens of soybean (Glycine max). An estimated annual worldwide loss of US$1–2 billion is caused by P. sojae, which was first identified as a soybean pathogen in the 1950s in Indiana, Ohio, and North Carolina (Schmitthenner, 1985; Tyler, 2007; Dorrance, 2018). The…
Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds
Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article PubMed PubMed Central Google Scholar Bankevich A, Nurk S,…
The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
Cutler, E. B. The Sipuncula: Their Systematics, Biology, And Evolution (New York: Cornell University Press, doi.org/10.7591/9781501723643, 1994) Nielsen, C. Some aspects of spiralian development. Acta Zool. 91, 20–28, doi.org/10.1111/j.1463-6395.2009.00421.x (2010). Article Google Scholar Huang, D. Y., Chen, J. Y., Vannier, J. & Saiz Salinas, J. I. Early Cambrian sipunculan worms…
Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation
Borzi, A. Le communicazioni intracellulari delle nostochinee. Malpighia – Rassegna mensuale di botanica 1 (1886–1887). Simon, R. D. Cyanophycin granules from the blue-green alga anabaena cylindrica: A reserve material consisting of copolymers of aspartic acid and arginine. Proc. Natl. Acad. Sci. U. S. A. 68, 265–267 (1971). Article ADS CAS …
Metagenomic insights into nutrient and hypoxic microbial communities at the macrofouling/steel interface leading to severe MIC
Structure of the macrofouling/steel interface Soft-fouling and hard-fouling organisms all could pose potential threats to marine facilities. Oysters, as representatives of hard-fouling organisms, are composed of a soft body protected by two complex shell sections. The oyster shell is primarily made of 97% calcium carbonate, which provides it with significant…
Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma
Holgate, S. T. et al. Asthma. Nat. Rev. Disease Primers 1, 15025. doi.org/10.1038/nrdp.2015.25 (2015). Article PubMed Google Scholar Juhn, Y. J. Risks for infection in patients with asthma (or other atopic conditions): is asthma more than a chronic airway disease?. J. Allergy Clin. Immunol. 134, 247–257. doi.org/10.1016/j.jaci.2014.04.024 (2014). Article PubMed …
The Biostar Herald for Tuesday, May 23, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
The roles and implications of RNA m6A modification in cancer
Huang, H., Weng, H. & Chen, J. m6A modification in coding and non-coding RNAs: roles and therapeutic implications in cancer. Cancer Cell 37, 270–288 (2020). Article CAS PubMed PubMed Central Google Scholar Qing, Y., Su, R. & Chen, J. RNA modifications in hematopoietic malignancies: a new research frontier. Blood 138,…
Sting and p53 DNA repair pathways are compromised in Alzheimer’s disease
Vemuri, P. et al. Evaluation of amyloid protective factors and Alzheimer disease neurodegeneration protective factors in elderly individuals. JAMA Neurol. 74(6), 718–726. doi.org/10.1001/jamaneurol.2017.0244 (2017) (Epub 2017/04/19). Article PubMed PubMed Central Google Scholar Soheili-Nezhad, S., van der Linden, R. J., Olde Rikkert, M., Sprooten, E. & Poelmans, G. Long genes are…
Screening/validation of pivotal pancreatic cancer gene DPYD
Introduction Pancreatic cancer (PC) is a malignant tumor with a very high mortality rate for which there is no effective treatment other than surgery.1,2 PC is prone to metastasis and invasion in the early stage, and there is no effective means for early detection. Most patients often have cancer metastasis…
Cleaved Amplified Polymorphic Sequence (CAPS)
Description CAPS are DNA fragments amplified by PCR using specific 20-25 bp primers, followed by digestion of the PCR products with a restriction enzyme. Subsequently, length polymorphisms resulting from variation in the occurrence of restriction sites are identified by gel electrophoresis of the digested products. CAPS have also been referred…
Naringenin ameliorates aluminum toxicity-induced testicular dysfunctions in mice by suppressing oxidative stress and histopathological alterations
Environmental aluminum intoxication has shown increasingly alarming negative consequences on reproductive health. This needs mechanistic exploration and preventive management using medicines like herbal supplementation. The ameliorative effects of naringenin (NAR) against AlCl3-induced reproductive toxicity were thus evaluated in this study by assessing testicular dysfunction in albino male mice. A group…
Genomic and phylogenetic analysis of Klebsiella michiganens
Introduction Multidrug-resistant Enterobacteriaceae infection is a severe threat to public health that is worsening globally and is associated with increasing mortality rates.1 Klebsiella pneumoniae is a significant pathogen that contributes to the dissemination of multidrug-resistant strains in healthcare environments.2 K. michiganensis is a novel specie of pathogenic Klebsiella genus. Since…
Quantitative DNA-RNA Immunoprecipitation Sequencing with Spike-Ins – PubMed DNA:RNA ImmunoPrecipitation and high-throughput sequencing.
doi: 10.1007/978-1-0716-2477-7_26. Memberships Expand Connections 1 Department about Chemical and Systems Biology, Stanford University, Stand-ford, CANCER, USA. [email protected] 2 Department of Chemical and Systems Nature, Stanford University, Stanford, CA, USA. [email protected] Freely PMC article Item in Clipboard Magdalena P Crossley et aluminium. Methods Mol Bil. 2022. Free PMC books Show details…
Indel driven rapid evolution of core nuclear pore protein gene promoters
Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783. doi.org/10.1146/annurev-biochem-062917-011901 (2019). Article CAS PubMed PubMed Central Google Scholar Cabal, G. G. et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441, 770–773 (2006)….
Antimicrobial activity of Limosilactobacillus fermentum strains isolated from the human oral cavity against Streptococcus mutans
Welch, J. L. M., Dewhirst, F. E. & Borisy, G. G. Biogeography of the oral microbiome: The site-specialist hypothesis. Annu. Rev. Microbiol. 73, 335–358. doi.org/10.1146/annurev-micro-090817-062503 (2019). Article CAS Google Scholar Cornejo Ulloa, P., van der Veen, M. H. & Krom, B. P. Review: Modulation of the oral microbiome by the…
Ancient gene linkages support ctenophores as sister to other animals
Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013). Article PubMed PubMed Central Google Scholar Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,…
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in Archaea
. 2023 May 16;rna.079636.123. doi: 10.1261/rna.079636.123. Online ahead of print. Affiliations Expand Affiliations 1 Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab & Regensburg Center for Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany. 2 Regensburg Center for Biochemistry, Biochemistry III –…
Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing
Introduction Perturbations in the infant gut microbiome during early life affect growth, development, and long-term health (Sherman, 2010; Carl et al., 2014; Tarr and Warner, 2016). Preterm infants have a physiologically and anatomically immature gastrointestinal tract that is known to be more permeable than that of term infants, and their…
Enrichr-KG: bridging enrichment analysis across multiple libraries
doi: 10.1093/nar/gkad393. Online ahead of print. Affiliations Expand Affiliation 1 Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA. Item in Clipboard John Erol Evangelista et al. Nucleic Acids Res. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/nar/gkad393….
Resistance of Nosocomial Acinetobacter baumannii
Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…
TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs
doi: 10.1093/nar/gkad355. Online ahead of print. Affiliations Expand Affiliation 1 Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland. Item in Clipboard Tomasz Woźniak et al. Nucleic Acids Res. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/nar/gkad355. Online ahead of print. Affiliation 1 Institute of Human Genetics,…
Long-Read Metagenomics and CAZyme Discovery
La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef CAS PubMed Google Scholar Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…
Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection
Global tuberculosis report 2020. (Geneva: World Health Organization; 2020. Licence: CC BY-NC-SA 3.0 IGO). Acuña-Villaorduna, C. et al. Intensity of exposure to pulmonary tuberculosis determines risk of tuberculosis infection and disease. Eur. Respir. J. 51, 1. doi.org/10.1183/13993003.01578-2017 (2018). Article Google Scholar Reichler, M. R. et al. Duration of exposure among…
Nontuberculous mycobacteria and MAB_0540 mutations
Introduction Nontuberculous mycobacteria (NTM), a mycobacterium other than the Mycobacterium tuberculosis complex (MTC) and M. leprae, are conditional pathogens widely found in the environment.1 Studies have shown that the probability of NTM transmission is extremely low, and exposure comes primarily from the environment, soil, water, etc.1 In recent years, lung…
Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity
World J Microbiol Biotechnol . 2023 May 3;39(7):179. doi: 10.1007/s11274-023-03631-2. Affiliations Expand Affiliations 1 Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India. 2 Department of Life Science and Bioinformatics, Hargobind Khurana School of Life Sciences, Assam University, Silchar, Assam, 788011, India. 3…
MTX Therapy Outcomes in Early Rheumatoid Arthritis
Introduction Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease, mainly characterised by symmetrical pain and swelling of small joints in the hands and the feet.1 When chronic inflammation is not properly controlled over a long period of time, it can eventually lead to irreversible damage to the joint structures….
Genome-Resolved Metagenomic Analysis of Nitrogen-Cycling Microbial Communities in Hydrologically Variable Floodplain Sediments from Riverton, Wyoming
Authors: Christopher A. Francis1* (caf@stanford.edu), Katie Langenfeld1, Anna Rasmussen1, Bradley B. Tolar1,5, Linta Reji1,6, Emily Cardarelli1,7, Zach Perzan1, Kristin Boye2, John R. Bargar3, Nicholas Bouskill4 Institutions: 1Stanford University, Stanford, CA; 2SLAC National Accelerator Laboratory, Menlo Park, CA; 3Pacific Northwest National Laboratory, Richland, WA; 4Lawrence Berkeley National Laboratory, Berkeley, CA; 5University…
Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone
Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Zinner D (2013) Hybridization and speciation. J Evolut Biol 26:229–246. doi.org/10.1111/j.1420-9101.2012.02599.x Article CAS Google Scholar Arntzen JW (2019) An amphibian species pushed out of Britain by a moving hybrid zone. Mol Ecol 28:5145–5154 Article PubMed PubMed Central Google…
Phenotypic and Genetic Analysis of KPC-49
Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…
RNA sequencing steps toward the first line
Editorial doi: 10.1002/cncr.34801. Online ahead of print. Affiliations Expand Affiliation 1 Department of Pathology, Moffitt Cancer Center, Tampa, Florida, USA. Item in Clipboard Editorial Theresa A Boyle et al. Cancer. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1002/cncr.34801. Online ahead of print. Affiliation 1 Department of Pathology, Moffitt…
Middle-out sequence confirmation of CRISPR/Cas9 single guide RNA (sgRNA) using DNA primers and ribonuclease T1 digestion
Pickar-Oliver A, Gersbach CA. The next generation of CRISPR–Cas technologies and applications. Nat Rev Mol Cell Bio. 2019;20:490–507. doi.org/10.1038/s41580-019-0131-5. Article CAS Google Scholar Hendel A, Bak RO, Clark JT, Kennedy AB, Ryan DE, Roy S, Steinfeld I, Lunstad BD, Kaiser RJ, Wilkens AB, Bacchetta R, Tsalenko A, Dellinger D, Bruhn…
Pathogenic mechanisms affecting mitochondrial DNA replication and transcription
1. Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression. Meenakshi Singh, Viktor Posse, Bradley Peter, Maria Falkenberg and Claes M. Gustafsson. Nucleic Acids Research, 2022, Vol. 50, No. 2, 989–999. doi.org/10.1093/nar/gkab1251 doi.org/10.1093/nar/gkab1251 2. POLRMT mutations impair mitochondrial transcription causing neurological disease. Monika Oláhová, Bradley Peter, Zsolt Szilagyi,…
The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
. 2023 Apr 18;5(2):lqad035. doi: 10.1093/nargab/lqad035. eCollection 2023 Jun. Affiliations Expand Affiliations 1 Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA. 2 Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Free PMC article Item in Clipboard Robert A Drewell et…
Primary Databases- Definition, Types, Examples, Uses
Modern genomic research generates vast amounts of raw sequence data, which has created the need for biological databases to store and organize this enormous data. Biological databases are collections of biological data that are used for the storage and organization of data in a way that facilitates easy retrieval of…
Revealing their global influence on health
Several studies have indicated the importance of gut microbes in maintaining human health. These microbes are also associated with fundamental physiologic processes, such as aging, drug response, nutrition, and pathophysiologic states (e.g., cardiovascular, metabolic, oncologic, neurological, and autoimmune diseases). To better understand the causal effects between gut microbes and disease…
Gene silencing of cytoskeleton-associated protein 5 in genetically unstable cancer cells
Physicochemical properties of siRNA-encapsulated LNPs and their endocytosis. (A) Structure of the ionizable lipid 10 used for LNP preparation. (B) Composition of the particles. (C) Average size (in nm), zeta potential (in mV), PDI (polydispersity index), and % encapsulation efficiency of the particles. Data are represented as mean ± SEM…
Expression profile of PRGs in gout patients
Introduction Gout is an inflammatory disease caused by the deposition of monosodium urate (MSU) crystals in joints and other non-joint tissues. The main clinical manifestations of gout include recurrent joint redness, swelling, heat and pain, and even joint mutilation, urinary acid nephropathy and renal failure.1,2 The incidence and prevalence of…
Research reveals molecular features of rare mtDNA mutations
A high-throughput single-cell single-mitochondrial genome sequencing technology known as iMiGseq has provided new insights into mutations of mitochondrial DNA (mtDNA) and offers a platform for assessing mtDNA editing strategies and genetic diagnosis of embryos prior to their implantation. An international team of researchers, led by KAUST stem cell biologist Mo…
New technology reveals hidden mitochondrial DNA mutations
A human blastocyst-like synthetic embryo called the blastoid, showing the presence of an enveloping layer of extraembryonic cells, a blastocoel-like cavity, epiblast cells (green, which produce the future embryo) and hypoblast cells (red, which produce the future embryo) . iMiGSeq was used to sequence mtDNA in a single blastoid to…
Biochemical studies of mitochondrial DNA maintenance and topology
Erdinc D, Macao M, Valenzuela S, Lesko N, Naess K, Peter B, Bruhn H, Wedell A, Wredenberg A and Falkenberg M. The disease-causing mutation p.F907I reveals a novel pathogenic mechanism for POL g-related diseases. Manuscript, 2023 Erdinc D,*, Rodríguez-Luis A,*, Fassad MR, Mackenzie S, Watson CM, Valenzuela S, Xie…
Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein
Olina, A. V., Kulbachinskiy, A. V., Aravin, A. A. & Esyunina, D. M. Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes. Biochem. 83, 483–497. doi.org/10.1134/S0006297918050024 (2018). Article CAS Google Scholar Wu, J., Yang, J., Cho, W. C. & Zheng, Y. Argonaute proteins: Structural features, functions and emerging…
New Technology Uncovers Hidden Mitochondrial DNA Mutations
A human blastocyst-like synthetic embryo called blastoid showing the presence of an enveloping layer of extra-embryonic cells, a blastocoel-like cavity, epiblast cells (green, giving rise to the future embryo) and hypoblast cells (red, giving rise to the future amnion). iMiGSeq was used to sequence mtDNA in a single blastoid to…
Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease
Rojansky R, Cha M-Y, Chan DC (2016) Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1. eLife 5:e17896. doi.org/10.7554/eLife.17896 CrossRef CAS PubMed PubMed Central Google Scholar Wei W, Pagnamenta AT, Gleadall N et al (2020) Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA…
Voltammetric and impedimetric analysis of adriamycin and fish sperm DNA interaction using pencil graphite electrodes
McGown LB, Joseph MJ, Pitner JB et al (1995) The nucleic acid ligand. A new tool for molecular recognition. Anal Chem 67:663A?8A. doi.org/10.1021/ac00117a002 Article CAS PubMed Google Scholar Topkaya SN, Cetin AE (2019) Determination of electrochemical interaction between 2-(1H-benzimidazol-2-yl) phenol and DNA sequences. Electroanalysis 31:1571?1578. doi.org/10.1002/elan.201900199 Article CAS Google Scholar …
Expanding known viral diversity in the healthy infant gut
Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article CAS PubMed PubMed Central Google Scholar Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…
Downregulated ESRP1/2 promotes lung metastasis of bladder carcinoma through altering FGFR2 splicing and macrophage polarization
Introduction Among all common noncutaneous malignancies, bladder carcinoma (BC) is the fourth prevalent one in all patients from the United States, and a subset of BC can progress to a severe muscle invasive form, leading to distal metastasis to other organs, including liver, lung, bone and mediastinum (1). BC with…
Quantitative haplotype-resolved analysis of mitochondrial DNA heteroplasmy in Human single oocytes, blastoids, and pluripotent stem cells
doi: 10.1093/nar/gkad209. Online ahead of print. Chongwei Bi 1 , Lin Wang 1 , Yong Fan 2 , Baolei Yuan 1 , Samhan Alsolami 1 , Yingzi Zhang 1 , Pu-Yao Zhang 3 , Yanyi Huang 4 5 , Yang Yu 3 6 , Juan Carlos Izpisua Belmonte 1 7 , Mo Li 1 8 Affiliations…
Single-cell individual full-length mtDNA sequencing by iMiGseq uncovers unexpected heteroplasmy shifts in mtDNA editing
doi: 10.1093/nar/gkad208. Online ahead of print. Chongwei Bi 1 , Lin Wang 1 , Yong Fan 2 , Baolei Yuan 1 , Gerardo Ramos-Mandujano 1 , Yingzi Zhang 1 , Samhan Alsolami 1 , Xuan Zhou 1 , Jincheng Wang 3 , Yanjiao Shao 4 , Pradeep Reddy 4 , Pu-Yao Zhang 5 , Yanyi Huang 3 6 , Yang Yu 5…
Role of the RNA-binding protein ZC3H41 in the regulation of ribosomal protein messenger RNAs in trypanosomes | Parasites & Vectors
Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 2002;30:1427–64. doi.org/10.1093/nar/30.7.1427. Article CAS PubMed PubMed Central Google Scholar Fernández-Moya SM, Estévez AM. Posttranscriptional control and the role of RNA-binding proteins in gene regulation in trypanosomatid protozoan parasites. Wiley Interdiscip Rev…
Gut Microbiota in Children with Hand Foot and Mouth Disease on 16S rRNA Gene Sequencing
Ooi MH, Wong SC, Lewthwaite P, Cardosa MJ, Solomon T (2010) Clinical features, diagnosis, and management of enterovirus 71. Lancet Neurol 9:1097–1105. doi.org/10.1016/S1474-4422(10)70209-X Article PubMed Google Scholar Aswathyraj S, Arunkumar G, Alidjinou E, Hober D (2016) Hand, foot and mouth disease (HFMD): emerging epidemiology and the need for a vaccine…
New model of DNA flexibility opens up the possibility of getting closer to the chromatin scale
In both physics and chemistry, the mesoscopic scale refers to the length scale on which the properties of a material or phenomenon can be studied, without entering into a discussion about the behavior of individual atoms. In a mesoscopic model, atomic scales are merged with the continuous scale, so they…
Klebsiella quasipneumoniae in intestine damages bile acid metabolism in hematopoietic stem cell transplantation patients with bloodstream infection | Journal of Translational Medicine
Almyroudis NG, Fuller A, Jakubowski A, Sepkowitz K, Jaffe D, Small TN, et al. Pre- and post-engraftment bloodstream infection rates and associated mortality in allogeneic hematopoietic stem cell transplant recipients. Transpl Infect Dis. 2005;7(1):11–7. Article CAS PubMed Google Scholar Auletta JJ. Current uses and outcomes of hematopoietic cell transplantation (HCT):…
Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
Cheng, P. et al. Prevalence and characteristic of swine-origin mcr-1-positive Escherichia coli in Northeastern China. Front Microbiol 12, 712707. doi.org/10.3389/fmicb.2021.712707 (2021). Article PubMed PubMed Central Google Scholar Liu, Y. Y. et al. Emergence of plasmid-mediated colistin resistance mechanism mcr-1 in animals and human beings in China: A microbiological and molecular…
Searching and Evaluating Publications and Preprints Using Europe PMC
Europe PMC in 2020. Ferguson C, Araújo D, Faulk L, Gou Y, Hamelers A, Huang Z, Ide-Smith M, Levchenko M, Marinos N, Nambiar R, Nassar M, Parkin M, Pi X, Rahman F, Rogers F, Roochun Y, Saha S, Selim M, Shafique Z, Sharma S, Stephenson D, Talo’ F, Thouvenin A,…
Linking prokaryotic genome size variation to metabolic potential and environment
Kirchberger PC, Schmidt ML, Ochman H. The ingenuity of bacterial genomes. Annu Rev Microbiol. 2020;74:815–34. Article CAS PubMed Google Scholar Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked…
Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
World Health Organization (2020) Lack of new antibiotics threatens global efforts to contain drug-resistant infections. World Health Organization, New release Geneva Google Scholar Kmietowicz Z (2017) Few novel antibiotics in the pipeline, WHO warns. BMJ: British Medical Journal (Online) 358:1. doi.org/10.1136/bmj.j4339 Article Google Scholar Falagas ME, Lourida P, Poulikakos P,…
Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome
Introduction Cyanide-containing compounds are known as nitriles and are widely distributed in the natural environment. They are generated by different plants in various forms, such as ricinine, phenyl acetonitrile, cyanogenic glycosides, and β -cyanoalanine (Sewell et al., 2003). Anthropogenic activities have substantially influenced the production of vast quantities of nitrile…
Scientists reveal protein synthesis mechanism in Giardia
Cryo-EM structure of the Giardia ribosome reveals a highly compact, GC-rich rRNA with eukaryotic r-proteins. (A) Structure of the Giardia ribosome with all the r-proteins colored (SSU, shades of blue and green; LSU, shades of red and purple) and labeled. (B) Four views (90° related) of the Giardia (top) and Saccharomyces…
Identification of hsa_circ_0001445 of a novel circRNA-miRNA-mRNA regulatory network as potential biomarker for coronary heart disease
Introduction Coronary heart disease (CHD) is the most common heart condition worldwide and the leading cause of death of elderly men and women (1). Despite recent declines in developed countries, both CHD morbidity and mortality continue to increase rapidly in developing countries. Various factors are involved in CHD pathogenesis, including…
SCRAPT: an iterative algorithm for clustering large 16S rRNA gene data sets
doi: 10.1093/nar/gkad158. Online ahead of print. Affiliations Expand Affiliations 1 Department of Computer Science, University of Maryland, College Park, 20742 MD, USA. 2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. Item in Clipboard Tu Luan et al. Nucleic Acids Res. 2023. Show details Display options Display…
Biology:Circular RNA databases and resources
In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life.[1][2][3] Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites…
Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem
Proctor, L. Priorities for the next 10 years of human microbiome research. Nature 569(7758), 623–625 (2019). Article ADS CAS PubMed Google Scholar Bahl, M. I., Bergström, A. & Licht, T. R. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis….
Profiling DNA Ligase Substrate Specificity with a Pacific Biosciences Single-Molecule Real-Time Sequencing Assay
Affiliations Expand Affiliations 1 University of Wisconsin-Madison, Madison, Wisconsin. 2 New England Biolabs, Ipswich, Massachusetts. Item in Clipboard Alexander T Duckworth et al. Curr Protoc. 2023 Mar. Show details Display options Display options Format AbstractPubMedPMID Affiliations 1 University of Wisconsin-Madison, Madison, Wisconsin. 2 New England Biolabs, Ipswich, Massachusetts. Item in Clipboard…
Portable rapid detection of maize chlorotic mottle virus using RT-RAA/CRISPR-Cas12a based lateral flow assay
Introduction Maize (Zea mays L.) is one of the most important cereal crops in the world. In 2011, a large outbreak of maize lethal necrosis disease (MLND) occurred in the Southern Rift Valley of Kenya (Wangai et al., 2012), caused up to 100% losses in maize yield, and affected the income…
Recombinant Anti-XRCC1 antibody [EPR4389(2)] (ab134056)
Overview Product name Description Rabbit monoclonal [EPR4389(2)] to XRCC1 Host species Rabbit Tested applications Suitable for: WB, IHC-P, ICC/IFmore detailsUnsuitable for: Flow Cyt or IP Species reactivity Reacts with: …
Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae
Crous, P. et al. Fungal planet description sheets: 107–127. Pers. Mol. Phylogeny Evol. Fungi 28, 138–182. doi.org/10.3767/003158512X652633 (2012). Article CAS Google Scholar Visentin, I. et al. Gnomoniopsis castanea sp. nov. (Gnomoniaceae, Diaporthales) as the causal agent of nut rot in sweet chestnut. J. Plant Pathol. 94, 411–419. doi.org/10.4454/JPP.FA.2012.045 (2012). Article …
Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils
1. Introduction Soil harbors high abundance and diversity of prokaryotic microorganisms, with 1 g of soil containing up to 10 billion microbial cells (Torsvik and Øvreås, 2002) and 103–106 phylotypes (Bickel and Or, 2020), including many microorganisms that play critical biogeochemical roles (Crowther et al., 2019). With continuous expansion of prokaryotic…
PCR detection of the pKM.19/ScrfI RFLP (D7S23), a marker closely linked to the cystic fibrosis mutation
Please use this identifier to cite or link to this item: hdl.handle.net/2445/42445 Title: PCR detection of the pKM.19/ScrfI RFLP (D7S23), a marker closely linked to the cystic fibrosis mutation Author: Nunes Martínez, VirginiaChillón, MiguelLench, N.Ramsay, M.Estivill, Xavier,…
Vancomycin-resistant E. faecium SJ2 strain carrying vanA
Introduction Enterococcus is a genus of Gram-positive, facultative anaerobe and oxidase-negative cocci classified as lactic acid bacteria and belonging to the Enterococcaceae family.1 Enterococci is a type of bacteria that is often found in the gastrointestinal tract of humans and other mammals.2,3 It comprises a ubiquitous group of bacteria that…
Mitochondrial C1QBP is essential for T cell antitumor function by maintaining mitochondrial plasticity and metabolic fitness
Liu X, Peng G (2021) Mitochondria orchestrate T cell fate and function. Nat Immunol 22:276–278. doi.org/10.1038/s41590-020-00861-6 Article CAS PubMed Google Scholar Buck MD, O’Sullivan D, Klein Geltink RI et al (2016) Mitochondrial dynamics controls T cell fate through metabolic programming. Cell 166:63–76. doi.org/10.1016/j.cell.2016.05.035 Article CAS PubMed PubMed Central Google Scholar …
Anti-CRISPR AcrIIC5 is a dsDNA mimic that inhibits type II-C Cas9 effectors by blocking PAM recognition
doi: 10.1093/nar/gkad052. Online ahead of print. Affiliations Expand Affiliations 1 Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. 2 Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing…
clinical prevention/treatment of infections caused by CR-PPE
Introduction Over the last decades, Proteus species infections have received special attention because of the emergence of some species resistant to various antimicrobial agents, particularly β-lactams.1 Proteus penneri, first recognized in 1982, is a member of the Enterobacteriaceae family, which is salicin- and esculin-negative and chloramphenicol-resistant.1,2 P. penneri is primarily…
Dual specificity and target gene selection by the MADS-domain protein FRUITFULL
Ludwig, L. S. et al. Transcriptional states and chromatin accessibility underlying human erythropoiesis. Cell Rep. 27, 3228–3240.e7 (2019). Article CAS PubMed PubMed Central Google Scholar Argelaguet, R. et al. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature 576, 487–491 (2019). Article CAS PubMed PubMed Central Google Scholar Pawlak, M….
Cyclic RNA switches that regulate gene expression in a cell type-specific manner
Schematic illustrations of circRNA switches and circuits. (A) Design of miRNA or protein-responsive circRNA switch. miRNA-responsive circRNA has the antisense of target miRNA sequence at the UTR. Protein-responsive circRNA has a protein-binding motif in IRES region. In both systems, gene expression from circRNA is repressed if the target miRNA or…
CAI in python: SeqUtils.CodonUsage vs CAI package
Hi I am trying to calculate the CAI (codon adaptation index) for a list of genes of interest. I decided to use the RSCU values from the Codon Bias database (CBDB), for the relative organism (B. subtilis 168): homepages.luc.edu/~cputonti/cbdb/genera/bacillus.html#s30 . I implemented a small python script to do so. While…
Developmental programming: adverse sexually dimorphic transcriptional programming of gestational testosterone excess in cardiac left ventricle of fetal sheep
Barker, D. J. Intrauterine programming of adult disease. Mol. Med. Today 1, 418–423 (1995). Article CAS PubMed Google Scholar Barker, D. J. The fetal and infant origins of disease. Eur. J. Clin. Investig. 25, 457–463 (1995). Article CAS Google Scholar Barker, D. J., Osmond, C., Golding, J., Kuh, D. &…
The Biostar Herald for Wednesday, February 15, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Traditional Mongolian Medicine Baolier Capsule
Introduction At present, major progress has been made to prevent and treat cardiovascular disease (CVD) through lifestyle changes and drugs, but CVD is still the main cause of death in humans, especially in developed country and developing country.1 It is worth noting that the residual risk of CVD in patients…
Multi-tissue landscape of somatic mtDNA mutations indicates tissue specific accumulation and removal in aging
Author Response Reviewer #1 (Public Review): The paper states that they observed a combined total of 77,017 single-nucleotide variants (SNVs) and 12,031 insertion/deletions (In/Dels) across all tissue, age, and intervention groups. Collectively, these data represent the largest collection of somatic mtDNA mutations obtained in a single study to date. However,…
Institut Pasteur MLST databases and software
LIN codes General presentation The cgMLST-based Life Identification Numbers (LIN) codes (cgLIN codes, or LIN codes for short) constitute the basis of a novel bacterial strain taxonomy system proposed in 2022. An implementation was initially developed for the Klebsiella pneumoniae species complex (KpSC) by Hennart et al. 2022. This system…
Powering Toxicogenomic Studies by Applying Machine Learning to Genomic Sequencing and Variant Detection
Alexandrov LB, Nik-Zainal S, Wedge DC et al (2013) Signatures of mutational processes in human cancer. Nature 500:415–421. doi.org/10.1038/nature12477 CrossRef CAS Google Scholar Alioto TS, Buchhalter I, Derdak S et al (2015) A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun 6:10001. doi.org/10.1038/ncomms10001 CrossRef CAS …
SLC7A11 is a prognostic biomarker in UCEC
Introduction Endometrial cancer (EC) is one of the most frequently diagnosed types of gynecological cancers, second only to cervical cancer in incidence.1 More than 50,000 women die from EC worldwide each year.2 Despite the development of diagnostic techniques and treatment means, the prognosis of advanced EC remains unsatisfactory.3,4 The therapeutic…
Draft genomes of Blastocystis subtypes from human samples of Colombia | Parasites & Vectors
Andersen LO, Bonde I, Nielsen HB, Stensvold CR. A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiol Ecol. 2015. doi.org/10.1093/femsec/fiv072. Article Google Scholar Audebert C, Even G, Cian A, Loywick A, Merlin S, Viscogliosi E, et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human…
Autochthonous Onchocerca lupi infection of a domestic dog in Austria | Parasites & Vectors
Grácio AJS, Richter J, Komnenou AT, Grácio MA. Onchocerciasis caused by Onchocerca lupi: an emerging zoonotic infection. Systematic review Parasitol Res. 2015;114:2401–13. doi.org/10.1007/s00436-015-4535-7 Article Google Scholar Bergua A, Hohberger B, Held J, Muntau B, Tannich E, Tappe D. Human case of Onchocerca lupi infection, Germany, August 2014. Euro Surveill. 2015;20:21099….
Leveraging 16S rRNA data to uncover vaginal microbial signatures in women with cervical cancer
1 Introduction Cervical cancer (CC) remains the fourth most common cancer in women worldwide, with 604,127 new cases in 2020 and more than 341,831 deaths, accounting for nearly 8% of all female cancer-related deaths annually (Sung et al., 2021). This common infection-related neoplasm and its premalignant precursor are caused by high-risk…
DNA replication study targets genes for antibiotic resistance
Model of Rep-mediated SaPI DNA initiation of replication. (A) The ATP-independent flexibility of CTD exposes the residues involved in iteron recognition. The diameter of the barrel in its N and C terminal sides might accommodate dsDNA. In (B), two hexamers have been speculatively depicted embracing dsDNA. Potential hexamer-hexamer interactions might…
Movements in proteins reveal information about antibiotic resistance spreading
The PriRep5 cryoEM structure. (A) The PriRep5 map processed in C1. Only the CTDs of subunits A, B and C were visible in the C1 map. Letters match the color code of subunits in (B). On the right, a transparent pink PriRep5 map processed in C6 and docked with the…
Potential Roles of mtDNA Mutations in PCOS-IR
Introduction Polycystic ovary syndrome (PCOS) is the most common endocrine disease occurring during reproductive years. It was a kind of endocrine and metabolic disorders that results in obesity, irregularity of menstruation, OS, hyperinsulinemia, hyperandrogenism, infertility, and sterility.1,2 First identified in 1935, PCOS was also recognized as Stein–Leventhal syndrome.3 Diagnosis of…
Epidemiology of Clostridioides difficile infection
Introduction Clostridioides difficile (C. difficile) is an anaerobic, gram-positive, spore-forming bacillus and important pathogen of antimicrobial-associated diarrhea and nosocomial diarrhea in humans.1 Clostridioides difficile infection (CDI) can progress from self-resolving diarrhea to colitis, life-threatening pseudomembranous colitis and toxic megacolon, and death.2,3 CDI is a toxin-mediated disease, and the major virulence…