@phdthesis{Pellegrino2022,
  author    = {Pellegrino, Antonio},
  title     = {miRNA profiling for diagnosis of chronic pain in polyneuropathy},
  doi       = {10.25932/publishup-58385},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-583858},
  school      = {Universit{\"a}t Potsdam},
  pages     = {viii, 97, xi},
  year      = {2022},
  abstract  = {This dissertation aimed to determine differential expressed miRNAs in the context of chronic pain in polyneuropathy. For this purpose, patients with chronic painful polyneuropathy were compared with age matched healthy patients. Taken together, all miRNA pre library preparation quality controls were successful and none of the samples was identified as an outlier or excluded for library preparation. Pre sequencing quality control showed that library preparation worked for all samples as well as that all samples were free of adapter dimers after BluePippin size selection and reached the minimum molarity for further processing. Thus, all samples were subjected to sequencing. The sequencing control parameters were in their optimal range and resulted in valid sequencing results with strong sample to sample correlation for all samples. The resulting FASTQ file of each miRNA library was analyzed and used to perform a differential expression analysis. The differentially expressed and filtered miRNAs were subjected to miRDB to perform a target prediction. Three of those four miRNAs were downregulated: hsa-miR-3135b, hsa-miR-584-5p and hsa-miR-12136, while one was upregulated: hsa-miR-550a-3p. miRNA target prediction showed that chronic pain in polyneuropathy might be the result of a combination of miRNA mediated high blood flow/pressure and neural activity dysregulations/disbalances. Thus, leading to the promising conclusion that these four miRNAs could serve as potential biomarkers for the diagnosis of chronic pain in polyneuropathy. Since TRPV1 seems to be one of the major contributors of nociception and is associated with neuropathic pain, the influence of PKA phosphorylated ARMS on the sensitivity of TRPV1 as well as the part of AKAP79 during PKA phosphorylation of ARMS was characterized. Therefore, possible PKA-sites in the sequence of ARMS were identified. This revealed five canonical PKA-sites: S882, T903, S1251/52, S1439/40 and S1526/27. The single PKA-site mutants of ARMS revealed that PKA-mediated ARMS phosphorylation seems not to influence the interaction rate of TRPV1/ARMS. While phosphorylation of ARMST903 does not increase the interaction rate with TRPV1, ARMSS1526/27 is probably not phosphorylated and leads to an increased interaction rate. The calcium flux measurements indicated that the higher the interaction rate of TRPV1/ARMS, the lower the EC50 for capsaicin of TRPV1, independent of the PKA phosphorylation status of ARMS. In addition, the western blot analysis confirmed the previously observed TRPV1/ARMS interaction. More importantly, AKAP79 seems to be involved in the TRPV1/ARMS/PKA signaling complex. To overcome the problem of ARMS-mediated TRPV1 sensitization by interaction, ARMS was silenced by shRNA. ARMS silencing resulted in a restored TRPV1 desensitization without affecting the TRPV1 expression and therefore could be used as new topical therapeutic analgesic alternative to stop ARMS mediated TRPV1 sensitization.},
  language  = {en}
}
@misc{CzarneckaWeicheltRoedigeretal.2022,
  author    = {Czarnecka, Malgorzata and Weichelt, Ulrike and R{\"o}diger, Stefan and Hanack, Katja},
  title     = {Novel Anti Double-Stranded Nucleic Acids Full-Length Recombinant Camelid Heavy-Chain Antibody for the Detection of miRNA},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-56914},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-569142},
  pages     = {1 -- 18},
  year      = {2022},
  abstract  = {The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection systems allow an easy onset handling compared to PCR or sequencing and can be considered as alternative methods to support miRNA diagnostic in the future. In this study, we describe the generation of a camelid heavy-chain-only antibody specifically recognizing miRNAs to establish an antibody-based detection method. The generation of nucleic acid-specific binders is a challenge. We selected camelid binders via phage display, expressed them as VHH as well as full-length antibodies, and characterized the binding to several miRNAs from a signature specific for dilated cardiomyopathy. The described workflow can be used to create miRNA-specific binders and establish antibody-based detection methods to provide an additional way to analyze disease-specific miRNA signatures.},
  language  = {en}
}
@article{CzarneckaWeicheltRoedigeretal.2022,
  author    = {Czarnecka, Malgorzata and Weichelt, Ulrike and R{\"o}diger, Stefan and Hanack, Katja},
  title     = {Novel Anti Double-Stranded Nucleic Acids Full-Length Recombinant Camelid Heavy-Chain Antibody for the Detection of miRNA},
  series = {International Journal of Molecular Sciences},
  volume    = {23},
  journal   = {International Journal of Molecular Sciences},
  edition   = {11},
  publisher = {MDPI},
  address   = {Basel, Schweiz},
  issn      = {1422-0067},
  doi       = {10.3390/ijms23116275},
  pages     = {1 -- 18},
  year      = {2022},
  abstract  = {The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection systems allow an easy onset handling compared to PCR or sequencing and can be considered as alternative methods to support miRNA diagnostic in the future. In this study, we describe the generation of a camelid heavy-chain-only antibody specifically recognizing miRNAs to establish an antibody-based detection method. The generation of nucleic acid-specific binders is a challenge. We selected camelid binders via phage display, expressed them as VHH as well as full-length antibodies, and characterized the binding to several miRNAs from a signature specific for dilated cardiomyopathy. The described workflow can be used to create miRNA-specific binders and establish antibody-based detection methods to provide an additional way to analyze disease-specific miRNA signatures.},
  language  = {en}
}
@article{Schmidt2017,
  author    = {Schmidt, Marco F.},
  title     = {miRNA Targeting Drugs},
  series = {Drug Target miRNA: Methods and Protocols},
  volume    = {1517},
  journal   = {Drug Target miRNA: Methods and Protocols},
  publisher = {Springer},
  address   = {New York},
  isbn      = {978-1-4939-6563-2},
  issn      = {1064-3745},
  doi       = {10.1007/978-1-4939-6563-2_1},
  pages     = {3 -- 22},
  year      = {2017},
  abstract  = {Only 20 years after the discovery of small non-coding, single-stranded ribonucleic acids, so-called microRNAs (miRNAs), as post-transcriptional gene regulators, the first miRNA-targeting drug Miravirsen for the treatment of hepatitis C has been successfully tested in clinical Phase II trials. Addressing miRNAs as drug targets may enable the cure, or at least the treatment of diseases, which presently seems impossible. However, due to miRNAs' chemical structure, generation of potential drug molecules with necessary pharmacokinetic properties is still challenging and requires a re-thinking of the drug discovery process. Therefore, this chapter highlights the potential of miRNAs as drug targets, discusses the challenges, and tries to give a complete overview of recent strategies in miRNA drug discovery.},
  language  = {en}
}
@article{OmidbakhshfardProostFujikuraetal.2015,
  author    = {Omidbakhshfard, Mohammad Amin and Proost, Sebastian and Fujikura, Ushio and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology},
  series = {Molecular plant},
  volume    = {8},
  journal   = {Molecular plant},
  number    = {7},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {1674-2052},
  doi       = {10.1016/j.molp.2015.01.013},
  pages     = {998 -- 1010},
  year      = {2015},
  abstract  = {Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level.},
  language  = {en}
}
@phdthesis{Devers2011,
  author    = {Devers, Emanuel},
  title     = {Phosphate homeostasis and novel microRNAs are involved in the regulation of the arbuscular mycorrhizal symbiosis in Medicago truncatula},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-55572},
  school      = {Universit{\"a}t Potsdam},
  year      = {2011},
  abstract  = {Die arbuskul{\"a}re Mykorrhiza ist die wahrscheinlich {\"a}lteste Form der Wurzelsymbiosen zwischen Pflanzen und Pilzen und hat sich vor 420 Millionen Jahren entwickelt. In dieser Symbiose, die zwischen nahezu allen Landpflanzen und Pilzen des Reiches Glomeromycota ausgebildet wird, versorgt der Pilz die Pflanze mit N{\"a}hrstoffen, wobei die verbesserte Versorgung mit Phosphat f{\"u}r die Pflanze sicher den gr{\"o}ßten Vorteil darstellt. Im Gegenzug erh{\"a}lt der Pilz Zucker, welche die Pflanze aus der Photosynthese bereitstellt. Zu hohe Phosphatkonzentrationen im Boden oder D{\"u}nger f{\"u}hren allerdings zu einer Verringerung in der Auspr{\"a}gung der arbuskul{\"a}ren Mykorrhiza. Diese Unterdr{\"u}ckung der Symbiose wird nicht durch eine lokale Reaktion der Wurzeln ausgel{\"o}st, sondern in erster Linie durch einen hohen Phosphatgehalt im Pflanzenspross. Somit handelt es sich also um eine systemische, also dem Gesamtsystem „Pflanze" betreffende Antwort. Die molekularen Mechanismen dieser Anpassung sind noch wenig bekannt und sind vor allem f{\"u}r die Agrarwirtschaft von besonderem Interesse. Eine Mikro-RNA (miRNA) des bereits bekannten Phosphathom{\"o}ostasesignalwegs (PHR1-miRNA399-PHO2 Signalweg) akkumuliert verst{\"a}rkt in mykorrhizierten Wurzeln. Das deutet daraufhin, dass dieser Signalweg und diese miRNA eine wichtige Rolle in der Regulation der arbuskul{\"a}ren Mykorrhiza spielen. Ziel dieser Studie war es neue Einblicke in die molekularen Mechanismen, die zur Unterdr{\"u}ckung der arbuskul{\"a}ren Mykorrhiza bei hohen Phosphatkonzentrationen f{\"u}hren, zu gewinnen. Dabei sollte der Einfluss von PHO2, sowie von miRNAs in dieser Symbiose genauer untersucht werden. Ein funktionelles Ortholog von PHO2, MtPho2, wurde in der Pflanze Medicago truncatula identifiziert. MtPho2-Mutanten, welche nicht mehr in der Lage waren ein funktionales PHO2 Protein zu exprimieren, zeigten schnellere Kolonisierung durch den AM-Pilz. Jedoch wurde auch in den mtpho2-Mutanten die Symbiose durch hohe Phosphatkonzentrationen unterdr{\"u}ckt. Dies bedeutet, dass PHO2 und somit der PHR1-miRNA399-PHO2 Signalweg eine wichtige Funktion w{\"a}hrend der fortschreitenden Kolonisierung der Wurzel durch den Pilz hat, aber und weitere Mechanismen in der Unterd{\"u}ckung der Symbiose bei hohen Phosphatkonzentrationen beteiligt sein m{\"u}ssen. Die Analyse von Transkriptionsprofilen von Spross- und Wurzeln mittels Microarrays zeigte, dass die Unterdr{\"u}ckung der AM Symbiose durch hohe Phosphatkonzentrationen m{\"o}glicherweise auf eine Unterdr{\"u}ckung der Expression einer Reihe symbiosespezifischer Gene im Spross der Pflanze beruht. Um die Rolle weiterer miRNA in der AM Symbiose zu untersuchen, wurden mittels einer Hochdurchsatz-Sequenzierung 243 neue und 181 aus anderen Pflanzen bekannte miRNAs in M. truncatula entdeckt. Zwei dieser miRNAs, miR5229 und miR160f*, sind ausschließlich w{\"a}hrend der arbuskul{\"a}ren Mykorrhiza zu finden und weitere miRNAs werden w{\"a}hrend dieser Symbiose verst{\"a}rkt gebildet. Interessanterweise f{\"u}hren einige dieser miRNAs zum Abbau von Transkripten, die eine wichtige Funktion in der arbuskul{\"a}ren Mykorrhiza und Wurzelkn{\"o}llchensymbiose besitzen. Die Ergebnisse dieser Studie liefern eine neue Grundlage f{\"u}r die Untersuchung von regulatorischen Netzwerken, die zur zellul{\"a}ren Umprogrammierung w{\"a}hrend der Interaktion zwischen Pflanzen und arbuskul{\"a}ren Mykorrhiza-Pilzen bei verschiedenen Phosphatbedingungen f{\"u}hren.},
  language  = {en}
}