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  1. Article: Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

    SHARMA, RAHUL

    BMC genomics, 17:537

    2016  

    Abstract: BACKGROUND: Bacteria within the genus Photorhabdus maintain mutualistic symbioses with nematodes in complicated lifecycles that also involves insect pathogenic phases. Intriguingly, these bacteria are rich in biosynthetic gene clusters that produce ... ...

    Institution Senckenberg Biodiversität und Klima Forschungszentrum
    Abstract BACKGROUND: Bacteria within the genus Photorhabdus maintain mutualistic symbioses with nematodes in complicated lifecycles that also involves insect pathogenic phases. Intriguingly, these bacteria are rich in biosynthetic gene clusters that produce compounds with diverse biological activities. As a basis to better understand the life cycles of Photorhabdus we sequenced the genomes of two recently discovered representative species and performed detailed genomic comparisons with five publically available genomes. RESULTS: Here we report the genomic details of two new reference Photorhabdus species. By then conducting genomic comparisons across the genus, we show that there are several highly conserved biosynthetic gene clusters. These clusters produce a range of bioactive small molecules that support the pathogenic phase of the integral relationship that Photorhabdus maintain with nematodes. CONCLUSIONS: Photorhabdus contain several genetic loci that allow them to become specialist insect pathogens by efficiently evading insect immune responses and killing the insect host.
    Keywords Secondary metabolites ; Sequencing ; Symbiosis ; Photorhabdus
    Language English
    Document type Article
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  2. Article: The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina

    SHARMA, RAHUL

    BMC genomics, 16:233

    2015  

    Abstract: BACKGROUND: Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the ... ...

    Institution Senckenberg Forschungsinstitut und Naturmuseum Frankfurt
    Senckenberg Biodiversität und Klima Forschungszentrum
    Abstract BACKGROUND: Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota. RESULTS: The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned. CONCLUSIONS: The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.
    Keywords Agaricomycotina ; Astaxanthin Synthase ; Fatty acid metabolism ; Fungal evolution ; Phylogeny ; Xanthophyllomyces dendrorhous
    Language English
    Document type Article
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  3. Article: Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

    SHARMA, RAHUL

    BMC genomics, 16:741

    2015  

    Abstract: BACKGROUND: Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic ... ...

    Institution Senckenberg Biodiversität und Klima Forschungszentrum
    Abstract BACKGROUND: Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. RESULTS: Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. CONCLUSIONS: The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
    Keywords Comparative genomics ; Core effectors ; Downy mildew ; Evolution ; Oomycetes ; Obligate biotroph ; Microsatellites ; Phytohormones ; Plant pathogen ; Promoters ; RxLR effectors
    Language English
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  4. Article ; Online: Structural Perspectives in the Development of Novel EGFR Inhibitors for the Treatment of NSCLC.

    Makhija, Rahul / Sharma, Anushka / Dubey, Rahul / Asati, Vivek

    Mini reviews in medicinal chemistry

    2024  

    Abstract: Non-small cell Lung cancer (NSCLC) is the most common type of lung cancer, which is caused by high consumption of tobacco and smoking. It is an epithelial lung cancer that affects about 2.2 million people across the globe, according to International ... ...

    Abstract Non-small cell Lung cancer (NSCLC) is the most common type of lung cancer, which is caused by high consumption of tobacco and smoking. It is an epithelial lung cancer that affects about 2.2 million people across the globe, according to International Agency for Research on Cancer (IARC). Non-small cell lung cancer is a malignant tumor caused by EGFR mutation that occurs in the in-frame deletion of exon 19 and L858R point mutation in exon 21. Presently, clinically available inhibitors of EGFR (including erlotinib, lapatinib, gefitinib, selumetinib, etc.) are not specific and responsible for undesirable adverse effects. Moreover, to solve this problem search for newer EGFR inhibitors is the utmost need for the treatment and/or management of increasing lung cancer burden. The discovery of therapeutic agents that inhibit the specific target in tumorous cells, such as EGFR, is one of the successful strategies in treating many cancer therapies, including lung cancer. The exhaustive literature survey (2018-2023) has shown the importance of medicinally privileged pyrimidine derivatives together, fused and/or clubbed with other heterocyclic rings to design and develop novel EGFR inhibitors. Pyrimidine derivatives substituted with phenylamine, indole, pyrrole, piperazine, pyrazole, thiophene, pyridine and quinazoline derivatives substituted with phenylamine, pyrimidine, morpholine, pyrrole, dioxane, acrylamide, indole, pyridine, furan, pyrimidine, pyrazole etc. are privileged heterocyclic rings shown promising activity by inhibiting EGFR and TKIs. The present review summarizes the structure-activity relationship (SAR) and enzyme inhibitory activity, including IC50 values, percentage inhibition, and kinetic studies of potential compounds from various literature. The review also includes various aspects of molecular docking studies with compounds under clinical trials and patents filed on pyrimidine-based EGFR inhibitors in treating non-small cell lung cancer. The present review may benefit the medicinal chemist for developing novel compounds such as EGFR inhibitors.
    Language English
    Publishing date 2024-04-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2104081-3
    ISSN 1875-5607 ; 1389-5575
    ISSN (online) 1875-5607
    ISSN 1389-5575
    DOI 10.2174/0113895575296174240323172754
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    Zs.A 5891: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article: Newborn Umbilical Cord Stump Myiasis: Report of an Earliest Presentation.

    Sharma, Shyam Bihari / Gupta, Rahul

    Journal of Indian Association of Pediatric Surgeons

    2023  Volume 28, Issue 1, Page(s) 86–87

    Language English
    Publishing date 2023-01-10
    Publishing country India
    Document type Journal Article
    ZDB-ID 2164528-0
    ISSN 1998-3891 ; 0971-9261
    ISSN (online) 1998-3891
    ISSN 0971-9261
    DOI 10.4103/jiaps.jiaps_125_22
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  6. Book ; Thesis: Auswertung der Qualitätssicherungsmaßnahmen nach Einführung eines Qualitätsmanagementsystems nach DIN EN ISO 9001:2000 am Interdisziplinären Uveitiszentrum Heidelberg

    Sharma, Rahul

    2005  

    Author's details vorgelegt von Rahul Sharma
    Language German
    Size III, 91, 78 Bl. : graph. Darst.
    Publishing country Germany
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Heidelberg, Univ., Diss., 2005
    HBZ-ID HT014648140
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2006 E 228 order for loan Magazin

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  7. Article ; Online: Tuning of surface oxygen vacancies for enhancing photocatalytic performance under visible light irradiation in Sb

    Sharma, Manisha / Singh, Rahul / Sharma, Anitya / Krishnan, Venkata

    Dalton transactions (Cambridge, England : 2003)

    2024  Volume 53, Issue 15, Page(s) 6731–6746

    Abstract: Tuning of vacancies in photocatalytic materials has emerged as a versatile strategy to enhance visible light absorption and photocatalytic activity. In this study, surface oxygen vacancies (defects) were incorporated on antimony tungstate to boost its ... ...

    Abstract Tuning of vacancies in photocatalytic materials has emerged as a versatile strategy to enhance visible light absorption and photocatalytic activity. In this study, surface oxygen vacancies (defects) were incorporated on antimony tungstate to boost its photocatalytic activity, which was examined by studying the degradation of model pollutants under visible light irradiation. Specifically, a two-to-three-fold increase in photocatalytic activity was observed for oxygen vacancy-rich antimony tungstate in comparison to its pristine counterpart. This improvement in the photocatalytic performance can be attributed to the presence of oxygen vacancies in the material, which leads to an enhanced absorption of light, decrease in the recombination of charge carriers, and increase in the number of active sites. In addition, owing to the nature of the surface charge present, the photocatalysts were found to be selective for the degradation of cationic pollutants in comparison to anionic and neutral pollutants, and can thus be used for the separation of a mixture of pollutants. Furthermore, scavenger studies illustrate that holes play a major role in the photocatalytic degradation of pollutants. Moreover, the excellent photostability of oxygen vacancy-rich antimony tungstate over three consecutive cycles demonstrates its potential as a good photocatalyst for the degradation of pollutants. Overall, this study demonstrates that the engineering of surface vacancies on perovskite oxide materials can render them as efficient single component photocatalysts for environmental remediation applications.
    Language English
    Publishing date 2024-04-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472887-4
    ISSN 1477-9234 ; 1364-5447 ; 0300-9246 ; 1477-9226
    ISSN (online) 1477-9234 ; 1364-5447
    ISSN 0300-9246 ; 1477-9226
    DOI 10.1039/d4dt00183d
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  8. Article: The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes

    Rühl, Martin / SHARMA, RAHUL / Thines, Marco

    BMC genomics, 19:48

    2018  

    Abstract: BACKGROUND: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of ...

    Institution Senckenberg Biodiversität und Klima Forschungszentrum
    Abstract BACKGROUND: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. RESULTS: Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. CONCLUSIONS: The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
    Keywords Comparative genomics ; Carbohydrate active enzymes ; Agaricales ; Basidiomycetes ; Developmental biology ; Fruit body ; Mushroom ; White-rot
    Language English
    Document type Article
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  9. Article ; Online: Analysis of energy storage materials for developments in solar cookers [version 2; peer review

    Rahul Goyal / Ravi Kumar Sharma / Rahul Khatri

    F1000Research, Vol

    2 approved]

    2023  Volume 11

    Abstract: Solar energy is accessible freely and can be utilized for many household and industrial applications. The consumption of solar energy for cooking applications has found significant success. Various innovations have been employed in facilitating cooking ... ...

    Abstract Solar energy is accessible freely and can be utilized for many household and industrial applications. The consumption of solar energy for cooking applications has found significant success. Various innovations have been employed in facilitating cooking during off-sunshine hours. Thermal energy storage helps in overcoming the fluctuations in the supply of energy required for cooking during different time periods of the day. This study focuses on the different types of thermal energy storage mediums that are currently utilized in solar cooking. Primarily, oils and pebbles are most commonly used as sensible heat storage (SHS) while organic phase change materials (PCMs) are used as latent heat thermal energy storage materials (LHTES). The properties and performances of various SHS and latent heat storage (LHS) mediums have been compared for their suitable utilization. SHS materials are cost-effective but have lower thermal gradient compared to LHTES materials. The energy storage capability of LHTES is high while degradation with the increasing number of charging and discharging cycles is also considerable. The melting point should be close to the utilization temperature for being used as LHTES as thermal diffusivity of the materials greatly influences the performance of solar cookers. The cooking time is lower for solar cooking systems equipped with energy storage compared to non-equipped cooking systems. It is recognized that the use of energy storage has been proved as a huge advantage to solar cooking systems, however, the design, and heat transfer characteristics of the cooking vessel along with the storage material type and volume must be optimized in order to make this technology more influential.
    Keywords Solar Energy ; Solar Cooker ; Energy Storage ; Sensible Heat ; Latent Heat ; Storage Capacity ; eng ; Medicine ; R ; Science ; Q
    Subject code 621
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Analysis of energy storage materials for developments in solar cookers.

    Khatri, Rahul / Goyal, Rahul / Sharma, Ravi Kumar

    F1000Research

    2023  Volume 11, Page(s) 1292

    Abstract: Solar energy is accessible freely and can be utilized for many household and industrial applications. The consumption of solar energy for cooking applications has found significant success. Various innovations have been employed in facilitating cooking ... ...

    Abstract Solar energy is accessible freely and can be utilized for many household and industrial applications. The consumption of solar energy for cooking applications has found significant success. Various innovations have been employed in facilitating cooking during off-sunshine hours. Thermal energy storage helps in overcoming the fluctuations in the supply of energy required for cooking during different time periods of the day. This study focuses on the different types of thermal energy storage mediums that are currently utilized in solar cooking. Primarily, oils and pebbles are most commonly used as sensible heat storage (SHS) while organic phase change materials (PCMs) are used as latent heat thermal energy storage materials (LHTES). The properties and performances of various SHS and latent heat storage (LHS) mediums have been compared for their suitable utilization. SHS materials are cost-effective but have lower thermal gradient compared to LHTES materials. The energy storage capability of LHTES is high while degradation with the increasing number of charging and discharging cycles is also considerable. The melting point should be close to the utilization temperature for being used as LHTES as thermal diffusivity of the materials greatly influences the performance of solar cookers. The cooking time is lower for solar cooking systems equipped with energy storage compared to non-equipped cooking systems. It is recognized that the use of energy storage has been proved as a huge advantage to solar cooking systems, however, the design, and heat transfer characteristics of the cooking vessel along with the storage material type and volume must be optimized in order to make this technology more influential.
    MeSH term(s) Humans ; Body Fluids ; Cooking ; Food ; Hot Temperature ; Patient Discharge
    Language English
    Publishing date 2023-02-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.126864.2
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