Unstill Life

This interdisciplinary project aims to reimagine the position of still life in the context of contemporary art. Derived from my memories and relationships with objects that represent my cultural background, this studio-based research traces my interest in visual perception. By intersecting analogue and digital media of art making, this project challenges the notion of stillness and expands on the idea of still life painting. Drawing from ideas of evocative objects, objecthood, stillness and expanded painting, this project opens dimensions of how still life is represented and experienced in contemporary diasporic art

Polycystic ovary syndrome: A disorder of reproductive age, its pathogenesis, and a discussion on the emerging role of herbal remedies

Polycystic ovary syndrome (PCOS) is a very common, complex, and heterogeneous endocrine disorder of women that involves a combination of environmental and genetic factors. PCOS affects women of growing age particularly at the early to late reproductive stage (15-35 years). Currently, PCOS affects 1 in every 10 women worldwide. It is characterized majorly by a raised level of androgens such as testosterone and a large number of ovarian cysts (more than 10) that cause anovulation, infertility, and irregular menstrual cycle. PCOS is also related to other endocrine and metabolic abnormalities, such as obesity, hirsutism, acne, diabetes, insulin resistance, and glucose impairment. PCOS can be treated with allopathic, ayurvedic, and natural or herbal medications along with lifestyle modifications. Herbal medicines remained in demand for numerous reasons such as high cost and side effects associated with the use of allopathic medicine and our traditional norms, which have helped humans to use more herbal products for their health benefits. Estrogenic and nonestrogenic phytochemicals present in various plant species such as Glycyrrhiza glabra L. [Fabaceae], Aloe vera (L.) Burm. f. [Asphodelaceae], Silybum marianum (L.). Gaertn. [Asteraceae], Serenoa repens (W.Bartram) Small [Arecaceae], Actaea racemosa L. [Ranunculaceae], and Angelica sinensis (Oliv.) Diels [Apiaceae] are effective and harmless. Herbal medicines are found to be cost-effective, efficacious, and a highly esteemed source of management/treatment for PCOS than allopathic medicines. In this literature review, diagnosis, signs, and symptoms of PCOS; causes of hormonal imbalance; and risk factors associated with PCOS and their management are discussed briefly, and the focus was to find out the role of herbal remedies in PCOS management

Artifizielle Evolution von katalytischen Nucleinsäuren und deren Anwendung für die Untersuchung von RNA

RNA molecules play diverse roles in biological systems. Post-transcriptional RNA modifications and dynamic structures enhance the functional diversity of RNA. A prerequisite for studying their biological significance is the availability of reliable methods for the detection of RNA modifications and structures. Several promising approaches have been developed in the last few decades; however, efficient, and versatile tools are still required to study the dynamic features of RNA. This thesis focuses on the development of nucleic acid catalysts as a tool to address the current needs in studying RNA. The major part of this thesis aimed at the development of deoxyribozymes as a tool for the detection of RNA modifications. Using in vitro selection from a random DNA library, we found deoxyribozymes that are sensitive to N 6 -isopentenyladenosine (i6A), a native tRNA modification and structural analogue of m6A. The in vitro evolution identified three classes of DNA enzymes: AA, AB08, and AC17 DNAzymes that showed distinct response to i6A modification and showed strong discrimination between structural analogues, i.e., m6A and i6A. In the continuation of the project, we attempted to develop RNA-cleaving deoxyribozymes that differentially respond to monomethylated cytidine isomers, 3-methylcytidine (m3C), N4 - methylcytidine (m4C), and 5-methylcytidine (m5C). Several deoxyribozymes were identified from in vitro selection, which are selective for a specific methylated cytidine isomer. The characterization of AL112, AM101, AN05, and AK104 catalysts confirmed the successful evolution of modification-specific and general deoxyribozymes that showed a broad substrate scope. In order to accelerate the DNAzymes discovery, a high throughput sequencing method (DZ-seq) was established that directly quantifies the RNA cleavage activity and cleavage site from deep sequencing data. The libraries contained information about cleavage status, cleavage site and sequence of deoxyribozymes and RNA substrate. The fraction cleaved (FC) data obtained from Dz-seq was validated for a subset of deoxyribozmes using conventional gel based kinetic assay and showed a good linear correlation (R2 = 0.91). Dz-seq possesses a great potential for the discovery of novel deoxyribozymes for the analysis of various RNA modifications in the future. The second objective of the current study was the development of structure-specific RNA labeling ribozymes. Here, we attempted to develop ribozymes that targets RNA of interest by structure-specific interaction rather than base-pairing and focused on a specific RNA G-quadruplex as the target. Two subsequent selection experiments led to the identification of the adenylyltransferase ribozymes AO10.2 and AR9. The partial characterization of these catalysts showed that A010.2 was unable to recognize intact BCL2 structure, but it turned out as the first reported trans-active ribozyme that efficiently labeled uridine in a defined substrate RNA hybridized to the ribozyme. The other ribozyme AR9 was shown to serve as a trans-active, self-labeling ribozyme that catalyzed adenylyl transferase reaction in the presence of the intact BCL2 sequence. Based on these preliminary findings, we envision that AR9 could potentially serve as a reporter RNA by self-labeling in the presence of an RNA G-quadruplex. However, both AO10.2 and AR9 still require more detailed characterization for their potential applications.RNA hat zahlreiche Funktionen in verschiedensten biologischen Systemen. Sowohl posttranskriptionelle Modifikationen als auch die Dynamik der dreidimensionalen Struktur von RNA trägt zu deren funktionalen Diversität bei. Eine Voraussetzung, um die biologische Bedeutung von RNA genauer zu untersuchen, ist die Verfügbarkeit zuverlässiger Methoden zur Detektion von RNA-Modifikationen und -Strukturen. In den letzten Jahrzenten wurden hierfür zahlreiche vielversprechende Ansätze entwickelt und berichtet. Allerdings besteht weiterhin der Bedarf an effizienten und vielseitig einsetzbaren Hilfsmitteln, um die Dynamik von RNA weiter zu erforschen. Diese Arbeit konzentriert sich auf die Entwicklung von Nucleinsäure basierten Katalysatoren, die in Zukunft als Werkzeug zur Untersuchung von RNA eingesetzt werden können. Der Großteil dieser Arbeit strebte die Entwicklung von Desoxyribozymen als Werkzeug für die Detektion von RNA-Modifikation an. Vor kurzem wurden m6A-sensitive DNA-Enzyme berichtet, die RNA schneiden können und damit Auskunft über deren Methylierungs-Status geben können. Diese sind auch in der Lage m6A in natürlichen RNAs wie lncRNAs und C/D box snoRNAs zu detektieren. Allerdings fehlen detaillierten strukturelle und mechanistische Erkenntnissen darüber, wie Desoxyribozyme solche Modifikationen detektieren. Deshalb ist es noch nicht möglich bereits vorhandene DNA-Enzyme umzuarbeiten, damit diese auch andere RNA-Modifikationen erkennen können. Aus diesem Grund fokussierten wir uns hier auf die Entwicklung neuer DNA-Enzyme für die Detektion von RNA-Modifikationen über m6A hinaus. Mit Hilfe von in vitro Selektion konnten wir ausgehend von einer randomisierten DNA-Bibliothek, Desoxyribozyme finden, die sensitiv gegenüber N6-Isopentenyladenosin (i6A) sind. Bei dieser Modifikation handelt es sich um ein strukturelles Analogon von m6A, die natürlicherweise in tRNA vorkommt. Als Ergebnis der in vitro Selektion konnten drei Klassen an DNA-Enzymen identifiziert werden: AA, AB08 und AC17 Desoxyribozyme. AA DNA-Enzyme spalteten unmodifizierte RNA und wurden durch i6A stark inhibiert. AB08 schnitten i6A-modifizierte RNA signifikant schneller als unmodifizierte RNA. Im Gegensatz hierzu zeigte AC17 ein einzigartiges Verhalten, indem es die Schneide-Position innerhalb der RNA um ein Nukleotid Richtung 5‘-Ende verschob, wenn eine i6A-Modifikation vorhanden war. Des weiteren konnten alle drei Klassen an DNA-Enzymen eindeutig zwischen m6A und i6A unterscheiden. Im weiteren Verlauf des Projektes strebten wir an RNA-schneidente Desoxyribozyme zu entwickeln, die die mono-methylierten Cytidin-Isomere 3-Methylcytidin (m3C), N4-Methylcytidin (m4C) und 5-Methylcytidine (m5C) voneinander unterscheiden können. Um vielseitigere DNA-Enzyme zu erhalten, benutzten wir RNA-Substrate, die ein randomisiertes Nukleotid in 5‘-Richtung neben dem methylierten Cytidin besaßen. Mehrere Desoxyribozyme konnten identifiziert werden, die selektiv und spezifisch für eines der methylierten Cytidin Isomere waren. Die Charakterisierung der DNA-Enzyme AL112, AM101, AN05 und AK104 bestätigte die erfolgreiche Evolution von einerseits modifikations-spezifischen sowie aber auch generellen DNA-Enzymen, die einen großen Substrat-Bereich abdecken. Zudem konnte gezeigt werden, dass AL112, AN05 und AK104 als programmierbare Werkzeuge zur Bestätigung von m3C- und m5C-Modifikationen in menschlicher mitochondrialen tRNA eingesetzt werden können. Um die Entdeckung von DNA-Enzymen weiter zu beschleunigen, wurde eine Hochdurchsatz-Sequenzierungsmethode (DZ-seq) entwickelt. Diese nutzt die Sequenzierungsdaten, um direkt die Schneideaktivität einzelner Desoxyribozyme zu quantifizieren sowie die genaue Stelle der RNA-Spaltung festzustellen. Illumina Sequenzierungsbibliotheken wurden ausgehend von aktiven DNA-Pools hergestellt, welche an bestimmte RNA-Substrate ligiert wurden. Nachdem die Schneide-Reaktion stattgefunden hatte, wurden sowohl die geschnittenen als auch die ungeschnittenen Fraktionen mit Hilfe von Poly(A)-Polymerase verlängert, woraufhin eine reverse Transkription mit Oligo-dT Primern folgte. Zu diesem Zeitpunkt beinhalteten die Bibliotheken bereits Informationen über den Schneide-Status, die exakte Schnittstelle innerhalb der RNA sowie über die Sequenzen des entsprechenden DNA-Enzyms und der Substrat-RNA. Die Daten, die durch Dz-Seq über die Schneideaktivität der einzelnen Desoxyribozyme erhalten wurden, wurde für einen Teil der Enzyme anhand konventioneller, gel-basierter kinetischer Assays validiert. Diese zeigten eine gute lineare Korrelation (R2 = 0.91). Interessanterweise zeigte Dz-Seq aber nur eine schwache Korrelation zwischen der Schneideaktivität und der Häufigkeit der Desoxyribozyme in der letzten Runde der in vitro Selektion. Zum Beispiel war AM301 nur zu einem geringen Anteil im DZ-seq Datensatz zu finden, war jedoch sehr aktiv. Dies ist nur ein Beispiel des großen Potentials von DZ-seq für die Entdeckung neuer DNA-Enzyme, die für die zukünftige Analyse zahlreicher RNA-Modifikationen angewendet werden könnten. Der zweite Teil dieser Arbeit beschäftigte sich mit der Entwicklung von Ribozymen, die spezifisch eine Ziel-RNA anhängig von deren Struktur markieren können. Die Inspiration hierfür stammt von den kürzlich berichteten Ribozymen FH14 und FJ1. Hierbei handelt es sich um Ribozyme, die über Watson-Crick-Basenpaarung ihre Ziel-RNA erkennen und diese dann sequenz-spezifisch markieren. Unser Ziel war es nun Ribozyme zu entwickeln, die ihre Ziel-RNA über Struktur-spezifische Wechselwirkungen anstelle von Basenpaarung erkennen. Hierbei fokussierten wir uns auf einen RNA G-Quadruplex als entscheidendes Strukturelement. Bei der in vitro Selektion wurde eine RNA Bibliothek verwendet, die kovalent an ein Fragment der 5‘-UTR der BCL2 RNA gebunden war. Von dieser RNA ist bekannt, dass sie einen G-Quadruplex formt. Zwei aufeinanderfolgende Selektionen führten zur Identifikation der Adenylyltransferasen AO10.2 und AR9. Die vorläufige Charakterisierung dieser beiden Ribozyme zeigte, dass AO10.2 die intakte BCL2-Struktur nicht erkennen kann. Stattdessen stellte sich heraus, dass dies das erste trans-aktive Ribozym ist, das effizient Uridin markieren kann, welches sich in einer definierten RNA-Struktur befindet, die mit dem Ribozym hybridisiert ist. Demnach hat es großes Potential als Werkzeug für die spezifische Markierung von RNA eingesetzt werden zu können. Beim zweiten Ribozym AR9 stellte sich heraus, dass es sich um ein trans-aktives, selbst-markierendes RNA-Enzym handelt, welches die gewünschte Reaktion nur bei Vorhandensein der intakten BCL2-Sequenz katalysiert. Basierend auf diesen vorläufigen Ergebnissen könnte AR9 als Reporter-RNA dienen, die sich RNA G-Quadruplexes selbst markiert. Allerdings benötigen sowohl AO10.2 als auch AR9 noch eine detailliertere Charakterisierung, bevor sie für potenzielle Anwendungen eingesetzt werden können

N6^6-Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes

RNA-cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site-specific endonuclease deoxyribozymes that selectively cleave posttranscriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. In this study, we report that the native tRNA modification N$^6$-isopentenyladenosine (i$^6$A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA-cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i$^6$A-modified RNA at least 2500-fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i$^6$A RNA modification. Together with deoxyribozymes that are strongly inhibited by i$^6$A, these results highlight intricate ways of modulating the catalytic activity of DNA by posttranscriptional RNA modifications

High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq)

RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states

In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications

Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart

RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA

Deoxyribozymes are emerging as modification-specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA-cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3-methylcytidine (m$^3$C), N$^4$-methylcytidine (m$^4$C), and 5-methylcytidine (m$^5$C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10- to 30-fold accelerated cleavage of their target m$^3$C-, m$^4$C- or m$^5$C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The m$^X$C-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m$^3$C and m$^5$C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites

Effect of Quinolones Versus Cefixime on International Normalized Ratio Levels After Valve Replacement Surgery with Warfarin Therapy

Background and Objectives: A dispute over interaction of warfarin with two quinolones—i.e., moxifloxacin and levofloxacin—leading to significant increase in international normalized ratio (INR) levels and coagulopathies is currently in debate. The study objective was to compare the INR values due to addition of quinolones and cefixime in warfarin treated patients after replacement of disease valves with metallic valves. Material and Methods: A prospective evaluation of patients who undergone valve replacement surgeries in the cardiology hospital setup in Pakistan during the period 2018–2019 was done, including all those subjects treated concurrently with levofloxacin, moxifloxacin, cefixime, and warfarin for the study. Data organized included demographic information, concurrent medications, and appropriate analytical parameters, especially INR values taken before and within seven days after prescribing three antibiotics in discharged patients who had undergone valve replacement surgeries. Patients for whom laboratory INR values were not given at the time of discharge and with deranged liver function, renal function, low albumin levels, and febrile patients were removed from study. Furthermore, patients were advised on possible food interactions and evaluated to examine if these factors have any possible influence on the interaction being studied. Results: Differences in INR were analyzed statistically by means of SPSS analysis before and after the possible interaction. Following the administration of levofloxacin and moxifloxacin to warfarin therapy, statistical analysis showed remarkable increase in INR (p < 0.001) and no significant change in INR was observed after cefixime treatment (p > 0.05). Conclusion: Results showed that, after adding levofloxacin and moxifloxacin in patients on warfarin, therapy contributed to remarkable increase in INR. However, addition of cefixime prevented frequent coagulopathies; therefore, close monitoring of INR and switching to a safe antibiotic such as cefixime is recommended

Evaluation of Clinical Outcomes After Remdesivir Therapy in Patients with Moderately Severe Covid-19 Disease. Prospective Study

Background Despite the fact that a number of therapeutic agents have been tested for the treatment of coronavirus disease 2019 (Covid-19), no antiviral agents have yet been proven to be effective.Objectives This study aims to evaluate the favorable clinical outcomes after remdesivir treatment in hospitalized patients with moderately severe COVID-19 disease in Pakistan.Methods A prospective study in hospitalized patients with moderately severe Covid-19 disease was conducted between January 2021- October 2021. The patients were divided into remdesivir-treated and control groups. The Remdesivir-treated group received 200mg IV, followed by 100mg once daily for four days. In addition to standard care, all patients received corticosteroid therapy. The clinical status of remdesivir patients was assessed after the 5th day of treatment, including proportion negative polymerase chain reaction test for COVID-19, length of hospitalization, improvement in oxygen demand, and effects on C-reactive protein (CRP) levels. Multivariate analysis and paired sample T-test were performed to evaluate a favorable response to remdesivir treatment and results were compared with a control group.Result In total, 328 patients were enrolled in the study, with 162 of them receiving IV remdesivir on the day of admission. The C-reactive protein level in the remdesivir treated group [median 22.0 (14.0-36.7)] was significantly lower (p<0.001) than in the remdesivir naive group [median 79.1 (57.4-139.0)]. The number of days spent in the hospital was significantly different between the remdesivir-treated and remdesivir-naive groups [6.2 0.5] (p<0.001). In the remdesivir-treated group, 36.7% of patients were discharged with a negative PCR, compared to 21.6% in the control group (p<0.001). In comparison to the control group, the remdesivir treated group showed a significant improvement in the ratio of arterial oxygen partial pressure to fractional inspired oxygen (p_<_0.001).Conclusion The remdesivir treatment was found to be superior to improve clinical outcomes among moderately severe Covid-19 disease patients