Tag: NAR

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…

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…

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;…

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…

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…

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…

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 …

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)…

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…

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…

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…

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,…

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…

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 …

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…

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 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…

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,…

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…

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…

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…

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…

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…

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…

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)….

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…

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,…

. 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, Universitätsstra&szlige 31, 93053 Regensburg, Germany. 2 Regensburg Center for Biochemistry, Biochemistry III –…

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…

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….

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…

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,…

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…

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…

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…

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…

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….

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…

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…

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…

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…

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…

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,…

. 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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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 …

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…

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…

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…

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…

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…

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…

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…

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):…

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…

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,…

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…

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,…

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…

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…

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…

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…

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…

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….

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…

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…

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: …

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 …

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…

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,…

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…

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 …

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…

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…

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….

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…

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…

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 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…

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…

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,…

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…

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 …

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…

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…

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….

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…

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…

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…

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…

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…