Tag: FEBS

A Simple Overview for Proteins Molecular Dynamics Simulations Using GROMACS

About Gromacs – Gromacs. s.d. Consulté le 5 mai 2023. www.gromacs.org/About_Gromacs Baker, D., Sali, A.: Protein structure prediction and structural genomics. Science 294(5540), 93–96 (2001). doi.org/10.1126/science.1065659 Beckstein, O., et al.: Ion channel gating: insights via molecular simulations. FEBS Lett. 555(1), 85–90 (2003). doi.org/10.1016/s0014-5793(03)01151-7 CrossRef  Google Scholar  Bowman, A.L., Ridder, L.,…

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Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics

Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82(11):801–11. Article  CAS  Google Scholar  Jeon SA, Park JL, Park SJ, Kim JH, Goh SH, Han JY, Kim SY. Comparison between MGI and Illumina sequencing platforms for whole genome sequencing. Genes Genomics. 2021;43(7):713–24. Article  CAS …

Continue Reading Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types | BMC Genomics

Characterization of the Spectrum of Mitochondrial DNA Nucleotide Substitutions in Human Populations in High Altitude Environments

Burtscher, J., Mallet, R.T., Pialoux, V., et al., Adaptive responses to hypoxia and/or hyperoxia in humans, Antioxid. Redox Signal., 2022, vol. 37, pp. 887—912. doi.org/10.1089/ars.2021.0280 Article  PubMed  Google Scholar  Chandel, N.S., McClintock, D.S., Feliciano, C.E., et al., Reactive oxygen species generated at mitochondrial complex III stabilize hypoxia-inducible factor-1alpha during hypoxia: a…

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Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Introduction In recent years, recombinant adenoviral vectors have been used in different fields of biomedical sciences such as in vitro and in vivo gene transfer, vaccine development, and gene therapy (Russell, 2000; Mitani and Kubo, 2002). Multiple features of recombinant adenoviral vectors such as high packaging capacity for transgene insertion,…

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Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout

FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar  Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article  Google Scholar  Hardy, R. W. Utilization of plant proteins in fish diets:…

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SOCS3 inhibiting JAK-STAT pathway enhances oncolytic adenovirus efficacy by potentiating viral replication and T-cell activation

Kaufman HL, Kohlhapp FJ, Zloza A. Oncolytic viruses: a new class of immunotherapy drugs. Nat Rev Drug Discov. 2015;14:642–62. Article  CAS  PubMed  PubMed Central  Google Scholar  Kessler T, Wick W. Oncolytic virotherapy: potentially a game-changing tumor treatment. Cancer Cell. 2021;39:753–5. Article  CAS  PubMed  Google Scholar  Koch J, Schober SJ, Hindupur…

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Cas9-induced targeted integration of large DNA payloads in primary human T cells via homology-mediated end-joining DNA repair

Khan, S. et al. Role of recombinant DNA technology to improve life. Int. J. Genomics Proteomics 2016, 2405954 (2016). Google Scholar  Spolski, R., Li, P. & Leonard, W. J. Biology and regulation of IL-2: from molecular mechanisms to human therapy. Nat. Rev. Immunol. 18, 648–659 (2018). Article  CAS  PubMed  Google…

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The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

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Regulation of the ER-Resident Mannosidase EDEM2 in HEK293 Cells

Abstract EDEM2 plays an important role as the first enzyme that acts during mannose trimming of N-glycosylated proteins in the ERAD machinery. Although EDEM2 expression has been reported to be transcriptionally regulated by the IRE1-sXBP1 pathway, very little is known about how endogenous EDEM2 protein expression is regulated. In this…

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Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts

Benjamin, E. J. et al. Heart disease and stroke statistics-2019 update: A report from the American Heart Association. Circulation 139, e56–e528 (2019). Article  PubMed  Google Scholar  Yusuf, S. et al. Effect of potentially modifiable risk factors associated with myocardial infarction in 52 countries (the INTERHEART study): Case-control study. Lancet 364,…

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A natural product YSK-A blocks SARS-CoV-2 propagation by targeting multiple host genes

Hoareau, L. & DaSilva, E. J. Medicinal plants: A re-emerging health aid. Electron. J. Biotechnol. 2, 3–4 (1999). Google Scholar  Jahan, I. & Ahmet, O. Potentials of plant-based substance to inhabit and probable cure for the COVID-19. Turk. J. Biol. 44, 228 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar …

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Preprint peer review gains momentum with new

4 December 2023 – Review Commons, a platform dedicated to the peer review of preprints, announces the expansion of its family of affiliate journals to include publications from three additional organizations. Affiliate journals accept the transfer of peer-reviewed preprints directly from the Review Commons online portal into their editorial workflow, where they are assessed…

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Mitophagy in human health, ageing and disease

Palikaras, K., Lionaki, E. & Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 20, 1013–1022 (2018). Article  CAS  PubMed  Google Scholar  Palikaras, K., Lionaki, E. & Tavernarakis, N. Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans. Nature 521, 525–528 (2015). Article …

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Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae | Nucleic Acids Research

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

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Germline PTEN genotype-dependent phenotypic divergence during the early neural developmental process of forebrain organoids

American Psychiatric Association Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5). Arlington, VA: American Psychiatric Publishing; 2013. Lewis MH, Bodfish JW. Repetitive behavior disorders in autism. Ment Retard Dev D R. 1998;4:80–9. Article  Google Scholar  Bodfish JW, Symons FJ, Parker DE, Lewis MH. Varieties of repetitive behavior in…

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Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis | Journal of Translational Medicine

Centore RC, Sandoval GJ, Soares LMM, Kadoch C, Chan HM. Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies. Trends Genet. 2020;36:936–50. Article  CAS  PubMed  Google Scholar  Pagliaroli L, Trizzino M. The Evolutionary conserved SWI/SNF subunits ARID1A and ARID1B Are Key modulators of pluripotency and cell-fate determination. Front Cell…

Continue Reading Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis | Journal of Translational Medicine

Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer

Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article  CAS  PubMed  PubMed Central  Google Scholar  Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article  CAS  PubMed  Google Scholar  Lawrence…

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Adipose cDC1s contribute to obesity-associated inflammation through STING-dependent IL-12 production

Ward, Z. J. et al. Projected U.S. state-level prevalence of adult obesity and severe obesity. N. Engl. J. Med. 381, 2440–2450 (2019). Article  PubMed  Google Scholar  Khaodhiar, L., McCowen, K. C. & Blackburn, G. L. Obesity and its comorbid conditions. Clin. Cornerstone 2, 17–31 (1999). Article  CAS  PubMed  Google Scholar …

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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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Association between mitochondrial DNA levels and depression: a systematic review and meta-analysis | BMC Psychiatry

Tartt AN, Mariani MB, Hen R, Mann JJ, Boldrini M. Dysregulation of adult hippocampal neuroplasticity in major depression: pathogenesis and therapeutic implications. Mol Psychiatry. 2022;27(6):2689–99. doi.org/10.1038/s41380-022-01520-y Article  CAS  PubMed  PubMed Central  Google Scholar  Friedrich MJ. Depression is the leading cause of disability around the World. JAMA. 2017;317(15):1517. doi.org/10.1001/jama.2017.3826 Article  PubMed …

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Establishment of a prognostic signature based on fatty acid metabolism genes in HCC associated with hepatitis B | BMC Gastroenterology

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global Cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71:209–49. Article  PubMed  Google Scholar  Chen W, Zheng R, Baade PD, Zhang S, Zeng H,…

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Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages

Rojas, J. M. & Santos, E. Ras-Gefs and Ras Gaps. In RAS Family GTPases Vol. 4 (Springer, 2006). Google Scholar  Broek, D. et al. The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell 48, 789–799 (1987). Article  CAS  PubMed  Google Scholar  van Dam, T. J. P., Rehmann,…

Continue Reading Transcriptomic analysis reveals that RasGEF1b deletion alters basal and LPS-induced expression of genes involved in chemotaxis and cytokine responses in macrophages

Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls

World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….

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Autophagy of the ER: the secretome finds the lysosome

Review doi: 10.1111/febs.16986. Online ahead of print. Affiliations Expand Affiliations 1 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA. 2 Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA. 3 Division of Metabolism, Endocrinology & Diabetes, Department of…

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Mechanisms of neurotransmitter transport and drug inhibition in human VMAT2

Kandel, E. R., Koester, J. D., Mack, S. H. & Siegelbaum, S. A. Principles of Neural Science 6th edn (McGraw Hill Professional, 2021). Ng, J., Papandreou, A., Heales, S. J. & Kurian, M. A. Monoamine neurotransmitter disorders—clinical advances and future perspectives. Nat. Rev. Neurol. 11, 567–584 (2015). Article  CAS  PubMed …

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Phase separation in cGAS-STING signaling

Sun L, Wu J, Du F, Chen X, Chen ZJ. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 2013; 339(6121): 786–791 Article  CAS  PubMed  Google Scholar  Wu J, Sun L, Chen X, Du F, Shi H, Chen C, Chen ZJ. Cyclic GMP-AMP…

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Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales

Quesada A, Vincent WF. Strategies of adaptation by antarctic cyanobacteria to ultraviolet radiation. Eur J Phycol. 1997;32:335–42. Article  Google Scholar  Genuário DB, Corrêa DM, Komárek J, Fiore MF. Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol. 2013;49:1142–53. Article  PubMed  Google Scholar  Makhalanyane TP, Valverde A, Gunnigle…

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Pseudogene MAPK6P4-encoded functional peptide promotes glioblastoma vasculogenic mimicry development

Gusyatiner, O. & Hegi, M. E. Glioma epigenetics: from subclassification to novel treatment options. Semin. Cancer Biol. 51, 50–58 (2018). Article  PubMed  Google Scholar  Kunnakkat, S. & Narayana, A. Bevacizumab in the treatment of high-grade gliomas: an overview. Angiogenesis 14, 423–430 (2011). Article  PubMed  Google Scholar  Luo, Q. et al….

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Crohn’s Disease treatment after failure of anti-TNF therapy

Introduction Crohn’s Disease (CD) is a typical group of inflammatory bowel disease, a chronic intestinal disease with an unclear cause that fluctuates between clinical remission and relapse. The disease may affect the entirety of the gastrointestinal tract, frequently manifesting as segmental, asymmetric, and transmural lesions. 21–47% of patients present with…

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The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection | Genome Biology

Dawson SJ, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013;368:1199–209. Massachusetts Medical Society. Article  CAS  PubMed  Google Scholar  van der Pol Y, Mouliere F. Toward the early detection of cancer by…

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Professor Caroline Dean awarded McClintock Prize

The ground-breaking career of Professor Dame Caroline Dean FRS has been recognised with the prestigious Barbara McClintock Prize for Plant Genetics and Genome Studies.  The international award is made to outstanding plant scientists working on genetics and genomics.   “I am thrilled and honoured to receive this award in recognition of…

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Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium

Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…

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ChromaCode Announces Landmark Peer-Reviewed Publication on Breakthrough HDPCR Assay for Non-Small-Cell Lung Cancer

CARLSBAD, Calif., Oct. 5, 2023 /PRNewswire/ — ChromaCode, Inc., a pioneering genomics multiplexing platform company developing accessible and affordable solutions for laboratories, patients and physicians, is proud to announce the publication of the first peer-reviewed demonstration of non-small-cell lung cancer (NSCLC) variant detection using ChromaCode’s groundbreaking High Definition PCR (HDPCR™)…

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Evaluation and validation of reference genes for RT-qPCR gene expression in Naegleria gruberi

Heggie, T. W. Swimming with death: Naegleria fowleri infections in recreational waters. Travel Med. Infect. Dis. 8, 201–206 (2010). Article  PubMed  Google Scholar  Grace, E., Asbill, S. & Virga, K. Naegleria fowleri: Pathogenesis, diagnosis, and treatment options. Antimicrob. Agents Chemother. 59, 6677–6681 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar …

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Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes

Li QS, Shabalin AA, DiBlasi E, Gopal S, Canuso CM, FinnGen ISGC, et al. Genome-wide association study meta-analysis of suicide death and suicidal behavior. Mol. Psychiatry 2023;28:891–900. McGuffin P, Marusic A, Farmer A. What can psychiatric genetics offer suicidology? Crisis. 2001;22:61–65. Article  CAS  PubMed  Google Scholar  Pedersen NL, Fiske A….

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When nature turns deadly: A look at Abrin

What is abrin? In certain parts of Asia and Australia, grows a flowering plant of the bean family Fabaceae, known as Abrus precatorius, also more commonly as jequirity bean or rosary pea [1]. It’s a delicate, perennial climber but extremely invasive and classified as a weed in several countries. However, what…

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A subpopulation of lipogenic brown adipocytes drives thermogenic memory

Farber, D. L., Netea, M. G., Radbruch, A., Rajewsky, K. & Zinkernagel, R. M. Immunological memory: lessons from the past and a look to the future. Nat. Rev. Immunol. 16, 124–128 (2016). Article  PubMed  Google Scholar  Netea, M. G. et al. Defining trained immunity and its role in health and…

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Precision RNA base editing with engineered and endogenous effectors

Gray, M. W. Evolutionary origin of RNA editing. Biochemistry 51, 5235–5242 (2012). Article  CAS  PubMed  Google Scholar  Covello, P. & Gray, M. On the evolution of RNA editing. Trends Genet. 9, 265–268 (1993). Article  CAS  PubMed  Google Scholar  Yablonovitch, A. L., Deng, P., Jacobson, D. & Li, J. B. The…

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Functional characterization of Alzheimer’s disease genetic variants in microglia

Nott, A. et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Neuner, S. M., Tcw, J. & Goate, A. M. Genetic architecture of Alzheimer’s disease. Neurobiol. Dis. 143, 104976 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar …

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Piet Borst Wins a Lasker Award for Scientific Excellence

Today (September 21), the Lasker Foundation announced the recipients of the 2023 Lasker Awards. Sometimes referred to as “America’s Nobels,” these prestigious awards recognize fundamental biological discoveries, clinical advances, and public advocacy for science.  Piet Borst, a physician-biochemist and molecular biologist at Netherlands Cancer Institute, received the Lasker~Koshland Award for…

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miRBase entry: hsa-mir-21

PubMed ID: 11679670 Identification of novel genes coding for small expressed RNAs “Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T”“Science (2001) 294:853-858 PubMed ID: 15183728 Human embryonic stem cells express a unique set of microRNAs “Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung…

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Remdesivir increases mtDNA copy number causing mild alterations to oxidative phosphorylation

Coronavirus disease (COVID-19) – World Health Organization. www.who.int/emergencies/diseases/novel-coronavirus-2019. Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409–424 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Kang, L. et al. A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Cell…

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Community-developed checklists for publishing images and image analyses

North, A. J. Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. J. Cell Biol. 172, 9–18 (2006). Article  CAS  PubMed  PubMed Central  Google Scholar  Brown, C. M. Fluorescence microscopy—avoiding the pitfalls. J. Cell Sci. 120, 1703–1705 (2007). Article  CAS  PubMed  Google Scholar  Senft, R. A. et…

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Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression

Andersson DI, Jerlstrom-Hultqvist J, Nasvall J (2015) Evolution of new functions de novo and from preexisting genes. Cold Spring Harb Perspect Biol 7:a017996 Article  PubMed  PubMed Central  Google Scholar  Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Auyeung VC, Ulitsky I, McGeary SE, Bartel…

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Genome-wide identification of lncRNA & mRNA for T2DM

Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia Correspondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email [email protected] Purpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with…

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Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249. doi.org/10.3322/caac.21660 (2021). Article  PubMed  Google Scholar  Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer statistics, 2022. CA A…

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RNA-sequencing and bioinformatics analysis | COPD

Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…

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Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties | CABI Agriculture and Bioscience

Anon. Human Development Report 1997. 1997. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43(W1):W39-49. doi.org/10.1093/NAR/GKV416. Article  CAS  PubMed  PubMed Central  Google Scholar  Balchin D, Hayer-Hartl M, Hartl FU. In vivo aspects of protein folding and quality control. Science. 2016;353(6294):aac4354. doi.org/10.1126/science.aac4354. Article  CAS  PubMed …

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Translation dysregulation in neurodegenerative diseases: a focus on ALS | Molecular Neurodegeneration

Tandan R, Bradley WG. Amyotrophic lateral sclerosis: part 1. Clinical features, pathology, and ethical issues in management. Annals of Neurology: Official Journal of the American Neurological Association and the Child Neurology Society. 1985;18:271–80. Article  CAS  Google Scholar  Mehta P et al. Prevalence of amyotrophic lateral sclerosis (ALS), United States, 2016….

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Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma

Swerdlow, S. H. et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. Blood 127, 2375–2390 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Sehn, L. H. & Salles, G. Diffuse large B-cell lymphoma. N. Engl. J. Med. 384, 842–858 (2021). Article  CAS  PubMed  PubMed Central …

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PARP14 correlates with GBM proliferation and poor prognosis by elevating expression of SAMD/SAMD9L

Jacob F, Salinas RD, Zhang DY et al (2020) A patient-derived glioblastoma organoid model and biobank recapitulates inter- and intra-tumoral heterogeneity. Cell 180(1):188–204 e122. doi.org/10.1016/j.cell.2019.11.036 Louis DN, Perry A, Wesseling P et al (2021) The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol 23(8):1231–1251….

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Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants

Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (New York, N.Y.) 337, 816–821 (2012). Article  CAS  PubMed  Google Scholar  Li, H., Li, J., Chen, J., Yan, L. & Xia, L. Precise modifications of both exogenous and endogenous genes in rice by prime editing. Mol….

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Comparative transcriptome profiling to unravel the key molecular signalling pathways and drought adaptive plasticity in shoot borne root system of sugarcane

Shrivastava, A. K. & Srivastava, S. Sugarcane: Physiological and molecular approaches for improving abiotic stress tolerance and sustaining crop productivity. (ed. Narendra Tuteja et al.) 885–992 (Wiley Blackell, Weinheim, 2012). Reyes, J. A. O., Casas, D. E., Gandia, J. L. & Delfin, E. F. Agricultural Research Updates Vol. 35 (ed…

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Computational optimization of antibody humanness and stability by systematic energy-based ranking

Raybould, M. I. J. et al. Thera-SAbDab: the therapeutic structural antibody database. Nucleic Acids Res. 48, D383–D388 (2020). Article  CAS  PubMed  Google Scholar  Schroff, R. W., Foon, K. A., Beatty, S. M., Oldham, R. K. & Morgan, A. C. Jr Human anti-murine immunoglobulin responses in patients receiving monoclonal antibody therapy….

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ctDNA and Lung Cancer | SpringerLink

Abbosh C, Birkbak NJ, Wilson GA, et al (2017) Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 545:446–451. doi.org/10.1038/nature22364 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Adalsteinsson VA, Ha G, Freeman SS, et al (2017) Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun…

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Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders

Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Gabriele, M., Tobon, A. L., D’Agostino, G. & Testa, G. The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog. Neuropsychopharmacol….

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Mutational Analysis Of Circulating Omicron SARS-CoV-2

Introduction SARS-CoV-2 is the most lethal virus among all human coronavirus (HCoV) and is responsible for causing severe respiratory tract infections.1,2 It was first reported in Wuhan, China, at the end of December 200193–5 and found to be highly transmissible (Basic reproduction number ranging from 0.9 to 6.53).4,6 The genome…

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Toxic and non-toxic dinoflagellates host distinct bacterial communities in their phycospheres

Moran, M. A. et al. Deciphering ocean carbon in a changing world. Proc. Natl. Acad. Sci. USA 113, 3143–3151 (2016). Article  CAS  Google Scholar  Ashraf, N., Ahmad, F. & Lu, Y. Synergy between microalgae and microbiome in polluted waters. Trends Microbiol. 31, 9–21 (2023). Article  CAS  Google Scholar  Ramanan, R….

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Selective activation of AKAP150/TRPV1 in ventrolateral periaqueductal gray GABAergic neurons facilitates conditioned place aversion in male mice

Ouyang, H. et al. An emerging new paradigm in opioid withdrawal: a critical role for glia-neuron signaling in the periaqueductal gray. Sci.World J. 2012, 940613–940613 (2012). Article  Google Scholar  Yeh, L. F., Ozawa, T. & Johansen, J. P. Functional organization of the midbrain periaqueductal gray for regulating aversive memory formation….

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Targeting miRNA by CRISPR/Cas in cancer: advantages and challenges | Military Medical Research

Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169(12):5429–33. Article  CAS  PubMed  PubMed Central  Google Scholar  Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in…

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Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia

Kraft B, Strous M, Tegetmeyer HE. Microbial nitrate respiration – genes, enzymes and environmental distribution. J Biotechnol. 2011;155:104–17. Article  CAS  PubMed  Google Scholar  Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. Article  CAS  PubMed  Google Scholar  Simon J, Klotz MG. Diversity and evolution of…

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Mutated Toll-like receptor 9 increases Alzheimer’s disease risk by compromising innate immunity protection

Cacace R, Sleegers K, Van Broeckhoven C. Molecular genetics of early-onset Alzheimer disease revisited. Alzheimers Dement. 2016;12:733–48. Article  PubMed  Google Scholar  Hoogmartens J, Cacace R, Van Broeckhoven C. Insight into the genetic etiology of Alzheimer’s disease: A comprehensive review of the role of rare variants. Alzheimers Dement (Amst). 2021;13:e12155. PubMed …

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Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor

Crutzen, P. J. The influence of nitrogen oxides on the atmospheric ozone content. Q. J. R. Meteorol. Soc. 96, 320–325 (1970). Article  Google Scholar  Johnston, H. Reduction of stratospheric ozone by nitrogen oxide catalysts from supersonic transport exhaust. Science 173, 517–522 (1971). Article  CAS  PubMed  Google Scholar  Hughes, M. N….

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Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1

Buckley, C. E. & St Johnston, D. Apical-basal polarity and the control of epithelial form and function. Nat. Rev. Mol. Cell Biol. 23, 559–577 (2022). Article  CAS  PubMed  Google Scholar  Buchheit, C. L., Weigel, K. J. & Schafer, Z. T. Cancer cell survival during detachment from the ECM: multiple barriers…

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Dissemination and genome characterization of a human adenovirus F41 in a patient with B-Cell lymphoma | Virology Journal

Lynch JP 3rd, Kajon AE. Adenovirus: Epidemiology, Global Spread of Novel types, and Approach to Treatment. Semin Respir Crit Care Med. 2021;42:800–21. Seto D, Chodosh J, Brister JR, Jones MS. Using the whole-genome sequence to characterize and name human adenoviruses. J Virol. 2011;85:5701–2. Article  CAS  PubMed  PubMed Central  Google Scholar …

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Intragenomic rDNA variation – the product of concerted evolution, mutation, or something in between?

Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8(2):135–141 Article  CAS  PubMed  Google Scholar  Ambrose CD, Crease TJ (2011) Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex. BMC Genet 12:13 Article  CAS  PubMed  PubMed Central …

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Regulation of the macrolide resistance ABC-F translation factor MsrD

Crowe-McAuliffe, C. et al. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. PNAS 115, 8978–8983 (2018). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Crowe-McAuliffe, C. et al. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat. Commun….

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Genetic diversity of Helicobacter pylori type IV secretion system cagI and cagN genes and their association with clinical diseases

Nabavi-Rad, A. et al. The interaction between autophagy, Helicobacter pylori, and gut microbiota in gastric carcinogenesis. Trends Microbiol. doi.org/10.1016/j.tim.2023.04.001 (2023). Article  Google Scholar  Nabavi-Rad, A. et al. The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management. Gut Microbes 14, 2108655 (2022). Article  PubMed Central  Google…

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Inhibition of the voltage-gated potassium channel Kv1.5 by hydrogen sulfide attenuates remodeling through S-nitrosylation-mediated signaling

Cherry, E. M. & Evans, S. J. Properties of two human atrial cell models in tissue: restitution, memory, propagation, and reentry. J Theor Biol 254, 674–690 (2008). Article  PubMed  PubMed Central  Google Scholar  Ozgen, N. & Rosen, M. R. Cardiac memory: a work in progress. Heart Rhythm 6, 564–570 (2009)….

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Low CO2 partial pressure steers CHO cells into a defective metabolic state

Blanco A, Burgos C, Gerez de Burgos NM, Montamat EE (1976) Properties of the testicular lactate dehydrogenase isoenzyme. Biochem J 153(2):165–172 Article  CAS  PubMed  PubMed Central  Google Scholar  Blombach B, Takors R (2015) CO2: intrinsic product, essential substrate, and regulatory trigger of microbial and mammalian production processes. Front Bioeng Biotechnol…

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Structural and functional analysis of a plant nucleolar RNA chaperone-like protein

Martinez-Seidel, F., Beine-Golovchuk, O., Hsieh, Y. C. & Kopka, J. Systematic review of plant ribosome heterogeneity and specialization. Front. Plant. Sci. 11, 948 (2020). Article  PubMed  PubMed Central  Google Scholar  Saez-Vasquez, J. & Delseny, M. Ribosome biogenesis in plants: From functional 45S ribosomal DNA organization to ribosome assembly factors. Plant…

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How long until effective Helicobacter pylori vaccine – human

Introduction Helicobacter pylori became a concern in 1979 when John Warren, a pathologist in Perth, Western Australia, discovered that the inflamed gastric mucosa was covered with bacteria that looked like Campylobacter.1 Warren and his colleague Barry Marshall cultured the first batch of these bacteria, newly named Helicobacter pylori, subsequently from…

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Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). Article  CAS  PubMed  Google Scholar  Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). Article …

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LSM2 is associated with a poor prognosis and promotes cell proliferation, migration, and invasion in skin cutaneous melanoma | BMC Medical Genomics

Rožanc J, Sakellaropoulos T, Antoranz A, Guttà C, Podder B, Vetma V, Rufo N, Agostinis P, Pliaka V, Sauter T et al. Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma. 2019; 26(8):1365–78. Schadendorf D, van Akkooi ACJ, Berking C, Griewank KG, Gutzmer R, Hauschild A, Stang…

Continue Reading LSM2 is associated with a poor prognosis and promotes cell proliferation, migration, and invasion in skin cutaneous melanoma | BMC Medical Genomics

Transforming Diagnosis and Therapeutics Using Cancer Genomics

Nogrady B (2020) How cancer genomics is transforming diagnosis and treatment. Nature 579(7800):S10–S10 CrossRef  CAS  PubMed  Google Scholar  Tabin CJ et al (1982) Mechanism of activation of a human oncogene. Nature 300(5888):143–149 CrossRef  CAS  PubMed  Google Scholar  Health NIO (2016) The human genome project completion: Frequently asked questions. National Human…

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Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei

Dahl, K. N., Ribeiro, A. J. S. & Lammerding, J. Nuclear shape, mechanics, and mechanotransduction. Circ. Res. 102, 1307–1318 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  Alisafaei, F., Jokhun, D. S., Shivashankar, G. V. & Shenoy, V. B. Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors…

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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…

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Transcriptomics and the origin of obligate parthenogenesis

Avise J (2008) Clonality: the genetics, ecology, and evolution of sexual abstinence in vertebrate animals. Oxford University Press, USA Book  Google Scholar  Avise JC (2015) Evolutionary perspectives on clonal reproduction in vertebrate animals. Proc Natl Acad Sci USA 112(29):8867–8873 Article  CAS  PubMed  PubMed Central  Google Scholar  Andrews S (2010) FastQC:…

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Expert Advice on CRISPR Design

  The following is an excerpt from an E-book that Twist developed for Genetic Engineering News: The Changing Landscape of CRISPR Screening: A guidebook to the latest CRISPR screening methodologies and technologies. You can download the full E-book here.   Even for seasoned researchers, designing an sgRNA library can be…

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Comparative analysis of bats and rodents’ genomes suggests a relation between non-LTR retrotransposons, cancer incidence, and ageing

Peona, V., Weissensteiner, M. H. & Suh, A. How complete are “complete” genome assemblies? An avian perspective. Mol. Ecol. Resour. 18, 1188–1195 (2018). Article  CAS  PubMed  Google Scholar  Peona, V. et al. Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise. Mol. Ecol….

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Analysis of tRNA-derived small RNAs

Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…

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Integrated analysis of circRNA-associated ceRNA in ischemic stroke

1 Introduction Stroke is the leading cause of permanent disability (Diener and Hankey, 2020). The latest global burden of disease (GBD) study (GBD 2019 Diseases and Injuries Collaborators, 2020) indicated that stroke is the leading cause of death in the Chinese population. The overall lifetime risk of stroke in China…

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Alterations of mtDNA copy number and 4977 bp deletion induced by ionizing radiation in human peripheral blood

Alterations of mtDNA copy number and 4977 bp deletion induced by ionizing radiation in human peripheral blood 2 first-author 1 1 1 3 1 1 3 corresp Corresponding author. E-mail address: lym636160@sina.com Corresponding author. E-mail address: lym636160@sina.com lym636160@sina.com Henan Institute of Occupational Medicine, Zhengzhou 450052, China Henan Institute of Occupational…

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Epigenetic regulation of human-specific gene expression in the prefrontal cortex | BMC Biology

Preuss TM. The human brain: rewired and running hot. Ann N Y Acad Sci. 2011;1225 Suppl 1(Suppl 1):E182-191. Article  PubMed  Google Scholar  Roth G, Dicke U. Evolution of the brain and intelligence in primates. Prog Brain Res. 2012;195:413–30. Article  PubMed  Google Scholar  Laland K, Seed A. Understanding human cognitive uniqueness….

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Selective control of parasitic nematodes using bioactivated nematicides

Tilman, D., Balzer, C., Hill, J. & Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260–20264 (2011). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Hunter, M. C., Smith, R. G., Schipanski, M. E., Atwood, L. W. & Mortensen, D….

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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…

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Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels

Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article  CAS  PubMed  Google Scholar  Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….

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Hallmarks of cardiovascular ageing | Nature Reviews Cardiology

Bergmann, O. et al. Evidence for cardiomyocyte renewal in humans. Science 324, 98–102 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  Senyo, S. E. et al. Mammalian heart renewal by pre-existing cardiomyocytes. Nature 493, 433–436 (2013). Article  CAS  PubMed  Google Scholar  Bergmann, O. et al. Dynamics of cell generation and…

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Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer’s disease

Cerejeira, J., Lagarto, L. & Mukaetova-Ladinska, E. B. Behavioral and psychological symptoms of dementia. Front. Neurol. 3, 73 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Murphy, M. P. & LeVine, H. III Alzheimer’s disease and the amyloid-beta peptide. J. Alzheimers Dis. 19, 311–323 (2010). Article  PubMed  PubMed Central  Google…

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Linkage between RFLP markers and genes affecting kernel hardness in wheat

American Association of Cereal Chemists (1989) Approved methods of the AACC: wheat hardness as determined by near-infrared reflectance. Method 39-70A, first approval August 1986, revised April 1987 and January 1989. The Association, St. Paul, Minnesota Google Scholar  Barlow KK, Buttrose MS, Simmonds DH, Vesk M (1973) The nature of the…

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Complete integration of carbene-transfer chemistry into biosynthesis

Arnold, F. H. Directed evolution: bringing new chemistry to life. Angew. Chem. Int. Ed. Engl. 57, 4143–4148 (2018). Article  CAS  PubMed  Google Scholar  Wallace, S. & Balskus, E. P. Interfacing microbial styrene production with a biocompatible cyclopropanation reaction. Angew. Chem. Int. Ed. Engl. 54, 7106–7109 (2015). Article  CAS  PubMed  PubMed…

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The origin and possible mechanism of embryonic cell-free DNA release in spent embryo culture media: a review

Menasha J, Levy B, Hirschhorn K, Kardon NB. Incidence and spectrum of chromosome abnormalities in spontaneous abortions: new insights from a 12-year study. Genet Med. 2005;7(4):251–63. doi.org/10.1097/01.GIM.0000160075.96707.04. Article  PubMed  Google Scholar  Munné S, Chen S, Collis P, Garrisi J, Zheng X, Cekleniak N, et al. Maternal age, morphology, development and…

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Adenylyl cyclase 6 plays a minor role in the mouse inner ear and retina

Boughman, J. A., Vernon, M. & Shaver, K. A. Usher syndrome: Definition and estimate of prevalence from two high-risk populations. J. Chronic Dis. 36, 595–603 (1983). Article  CAS  PubMed  Google Scholar  Hartong, D. T., Berson, E. L. & Dryja, T. P. Retinitis pigmentosa. Lancet 368, 1795–1809 (2006). Article  CAS  PubMed …

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Whole-exome sequencing in Chinese Tibetan patients with VSD

Introduction Congenital heart disease (CHD) refers to cardiovascular malformations caused by abnormal development of cardiac vessels during the fetal period, which is the most common congenital dysplasia and also the main cause of non-infectious death in newborns and infants.1 CHD includes atrial septal defect (ASD), ventricular septal defect (VSD), pulmonary…

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Revolutionizing Glycobiology: A Mass Spectrometrist’s Perspective

In this interview conducted at Pittcon 2023 in Philadelphia, Pennsylvania, we spoke to Professor Albert Heck and gained a mass spectrometrist’s perspective on the field of glycobiology.  What is your professional background, and what first attracted you to the field that you work within? My name is Albert Heck, and I…

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Comprehensive analysis of circular RNAs in porcine small intestine epithelial cells associated with susceptibility to Escherichia coli F4ac diarrhea | BMC Genomics

Ren J, Yan X, Ai H, Zhang Z, Huang X, Ouyang J, Yang M, Yang H, Han P, Zeng W, et al. Susceptibility towards enterotoxigenic Escherichia coli F4ac diarrhea is governed by the MUC13 gene in pigs. PLoS ONE. 2012;7(9):e44573. Article  CAS  PubMed  PubMed Central  Google Scholar  Guinée P, Jansen…

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The therapeutic potential of neurofibromin signaling pathways and binding partners

Bergqvist, C. et al. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J. Rare Dis. 15, 1–23 (2020). Article  Google Scholar  Martin, G. A. et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell 63, 843–849 (1990)….

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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…

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Prostatitis as initial manifestation of Chlamydia psittaci pneumonia diagnosed by metagenome next-generation sequencing: A case report

References [1] Hogerwerf L, Roof I, de Jong MJK, Dijkstra F, van der Hoek W. Animal sources for zoonotic transmission of psittacosis: A systematic review. BMC Infect Dis. 2020;20(1):192.Search in Google Scholar [2] Stokes HS, Berg ML, Bennett ATD. A review of chlamydial infections in wild birds. Pathogens. 2021;10(8):948.Search in…

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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…

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