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Kufner CL, Krebs S, Fischaleck M, Philippou-Massier J, Blum H, Bucher DB, Braun D, Zinth W, Mast CB. Sequence dependent UV damage of complete pools of oligonucleotides. Sci Rep 2023; 13:2638. [PMID: 36788271 PMCID: PMC9929323 DOI: 10.1038/s41598-023-29833-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.
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Affiliation(s)
- Corinna L. Kufner
- grid.38142.3c000000041936754XHarvard-Smithsonian Center for Astrophysics, Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, MA 02138 USA
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Marlis Fischaleck
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Julia Philippou-Massier
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dominik B. Bucher
- grid.6936.a0000000123222966Chemistry Department, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Dieter Braun
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Wolfgang Zinth
- grid.5252.00000 0004 1936 973XBiomolecular Optics and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
| | - Christof B. Mast
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
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Kumari S, Kumar V, Tiwari RK, Ravidas V, Pandey K, Kumar A. - Amphotericin B: A drug of choice for Visceral Leishmaniasis. Acta Trop 2022; 235:106661. [PMID: 35998680 DOI: 10.1016/j.actatropica.2022.106661] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2022]
Abstract
Visceral leishmaniasis or Kala-azar is a vector-borne disease caused by an intracellular parasite of the genus leishmania. In India, Amphotericin B (AmB) is a first-line medication for treating leishmaniasis. After a large-scale resistance to pentavalent antimony therapy developed in Bihar state, it was rediscovered as an effective treatment for Leishmania donovani infection. AmB which binds to the ergosterol of protozoan cells causes a change in membrane integrity resulting in ions leakage, and ultimately leading to cell death. The treatment effect of liposomal AmB can be seen more quickly than deoxycholate AmB because, it has some toxic effects, but liposomal AmB is significantly less toxic. Evidence from studies suggested that ABLC (Abelcet) and ABCD (Amphotec) are as effective as L-AmB but Liposomal form (Ambisome) is a more widely accepted treatment option than conventional ones. Nevertheless, the world needs some way more efficient antileishmanial drugs that are less toxic and less expensive for people living with parasitic infections caused by Leishmania. So, academics, researchers, and sponsors need to focus on finding such drugs. This review provides a summary of the chemical, pharmacokinetic, drug-target interactions, stability, dose efficacy, and many other characteristics of the AmB and their various formulations. We have also highlighted the clinically significant aspects of PKDL and VL co-infection with HIV/TB.
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Affiliation(s)
- Shobha Kumari
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, Bihar, India
| | - Vikash Kumar
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, Bihar, India
| | - Ritesh Kumar Tiwari
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, Bihar, India
| | - Vidyanand Ravidas
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, Bihar, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, Bihar, India
| | - Ashish Kumar
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, Bihar, India.
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Al-Khalaifah HS. Major Molecular Factors Related to Leishmania Pathogenicity. Front Immunol 2022; 13:847797. [PMID: 35769465 PMCID: PMC9236557 DOI: 10.3389/fimmu.2022.847797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Leishmaniasis is a major health problem with 600k - 1M new cases worldwide and 1 billion at risk. It involves a wide range of clinical forms ranging from self-healing cutaneous lesions to systemic diseases that are fatal if not treated, depending on the species of Leishmania. Leishmania sp. are digenetic parasites that have two different morphological stages. Leishmania parasites possess a number of invasive/evasive and pathoantigenic determinants that seem to have critical roles in Leishmania infection of macrophages which leads to successful intracellular parasitism in the parasitophorous vacuoles. These determinants are traditionally known as “virulence factors”, and are considered to be good targets for developing specific inhibitors to attenuate virulence of Leishmania by gene deletions or modifications, thus causing infective, but non-pathogenic mutants for vaccination. Pathway of biosynthesis is critical for keeping the parasite viable and is important for drug designing against these parasites. These drugs are aimed to target enzymes that control these pathways. Accordingly, maintaining low level of parasitic infection and in some cases as a weapon to eradicate infection completely. The current paper focuses on several virulence factors as determinants of Leishmania pathogenicity, as well as the metabolites produced by Leishmania to secure its survival in the host.
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Poveda A, Méndez MÁ, Armijos-Jaramillo V. Analysis of DNA Polymerases Reveals Specific Genes Expansion in Leishmania and Trypanosoma spp. Front Cell Infect Microbiol 2020; 10:570493. [PMID: 33117729 PMCID: PMC7576959 DOI: 10.3389/fcimb.2020.570493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/02/2020] [Indexed: 01/01/2023] Open
Abstract
Leishmaniasis and trypanosomiasis are largely neglected diseases prevailing in tropical and subtropical conditions. These are an arthropod-borne zoonosis that affects humans and some animals and is caused by infection with protozoan of the genera Leishmania and Trypanosoma, respectively. These parasites present high genomic plasticity and are able to adapt themselves to adverse conditions like the attack of host cells or toxicity induced by drug exposure. Different mechanisms allow these adapting responses induced by stress, such as mutation, chromosomal rearrangements, establishment of mosaic ploidies, and gene expansion. Here we describe how a subset of genes encoding for DNA polymerases implied in repairing/translesion (TLS) synthesis are duplicated in some pathogenic species of the Trypanosomatida order and a free-living species from the Bodonida order. These enzymes are both able to repair DNA, but are also error-prone under certain situations. We discuss about the possibility that these enzymes can act as a source of genomic variation promoting adaptation in trypanosomatids.
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Affiliation(s)
- Ana Poveda
- DNA Replication and Genome Instability Unit, Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Salud Pública y Zoonosis-CIZ, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador.,Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Burjassot, Spain
| | - Miguel Ángel Méndez
- Grupo de Química Computacional y Teórica, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Grupo de Bio-Quimioinformática, Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
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Rico-San Román L, Horcajo P, Regidor-Cerrillo J, Fernández-Escobar M, Collantes-Fernández E, Gutiérrez-Blázquez D, Hernáez-Sánchez ML, Saeij JPJ, Ortega-Mora LM. Comparative tachyzoite proteome analyses among six Neospora caninum isolates with different virulence. Int J Parasitol 2020; 50:377-388. [PMID: 32360428 DOI: 10.1016/j.ijpara.2020.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/30/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
Abstract
The biological variability among Neospora caninum isolates has been widely shown, however, the molecular basis that determines this diversity has not been thoroughly elucidated to date. The latest studies have focused on a limited number of isolates. Therefore, the goal of the present study was to compare the proteome of a larger number of N. caninum isolates with different origins and virulence. Label-free LC-MS/MS was used to investigate the tachyzoite proteomic differences among Nc-Bahia, Nc-Spain4H and Nc-Spain7, representing high virulence isolates and Nc-Ger6, Nc-Spain2H and Nc-Spain1H, representing low virulence isolates. Pairwise comparisons between all isolates and between high virulence and low virulence groups identified a subset of proteins with higher abundance in high virulence isolates. These proteins were involved in energy and redox metabolism, and DNA/RNA processing, which might determine the faster growth rates and parasite survival of the high virulence isolates. Highlighted proteins included a predicted member of the rhoptry kinase family ROP20 specific for N. caninum, Bradyzoite pseudokinase 1 and several dense granule proteins. DNA polymerase, which was more abundant in all high virulence isolates in all comparisons, might also be implicated in virulence. These results reveal insights into possible mechanisms involved in specific phenotypic traits and virulence in N. caninum, and the relevance of these candidate proteins for N. caninum virulence deserves further investigation.
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Affiliation(s)
- Laura Rico-San Román
- SALUVET, Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Pilar Horcajo
- SALUVET, Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Javier Regidor-Cerrillo
- SALUVET, Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain; SALUVET-Innova S.L., Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Mercedes Fernández-Escobar
- SALUVET, Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Esther Collantes-Fernández
- SALUVET, Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Dolores Gutiérrez-Blázquez
- Proteomics Unit of Complutense University of Madrid, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - María Luisa Hernáez-Sánchez
- Proteomics Unit of Complutense University of Madrid, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Jeroen P J Saeij
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA
| | - Luis Miguel Ortega-Mora
- SALUVET, Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain.
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Esmaeeli S, Hoseinirad SM, Rajabian M, Taheri AR, Berenji F, Hashemy SI. Evaluation of the oxidant-antioxidant balance, isoprostane and quantitative CRP in patients with cutaneous leishmaniasis. Microb Pathog 2019; 137:103738. [PMID: 31513893 DOI: 10.1016/j.micpath.2019.103738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/02/2019] [Accepted: 09/08/2019] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Cutaneous leishmaniasis is a dermal disease caused by several species of the genus Leishmania. It is an endemic disease with 1.2 million new cases occurring annually and mostly in developing countries. Oxidative stress is a condition of an imbalance in oxidant/antioxidant which may play a role in many different pathologic conditions. For the first time in this study, we introduced isoprostane as a reliable index for oxidative stress in patients suffering from leishmaniasis. We also investigated the possible relation between quantitative CRP and this disease. METHOD AND MATERIAL We collected 5 ml blood of 30 patients in addition to the same sample of the control healthy group. After applying appropriate methods, the plasma and serum specimens were extracted in order to conduct oxidant-antioxidant balance and CRP tests in serum as well as measuring isoprostane factor in plasma. STATISTICAL ANALYSIS We used T-student, ANOVA as well as linear regression to analyze the gathered data with a 0.05 confidence interval in SPSS environment. RESULTS The results showed a significant difference between the two groups in terms of the oxidant-antioxidant balance. Also, isoprostane and quantitative CRP levels were substantially higher in patients. There was no significant relationship between the mentioned factors and wound size and number. CONCLUSION Leishmania Amastigotes plays an important role in disturbing the oxidant-antioxidant balance resulting in inflammation and stress in patients. Furthermore, isoprostane was confirmed as a reliable index for evaluating oxidative stress in patients.
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Affiliation(s)
- Sara Esmaeeli
- Department of Clinical Biochemistry, Faculty of Medicine,d Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Hoseinirad
- Department of Clinical Biochemistry, Faculty of Medicine,d Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Rajabian
- Department of Biochemistry, Payame-Noor University, Mashhad, Iran
| | - Ahmad Reza Taheri
- Department of Dermatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fariba Berenji
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Isaac Hashemy
- Department of Clinical Biochemistry, Faculty of Medicine,d Mashhad University of Medical Sciences, Mashhad, Iran; Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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