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  • 51.
    Stangeland, Biljana
    et al.
    Plant Molecular Biology Laboratory, Department of Plant and Environmental Sciences, University of Life Sciences, PO Box 5003, N-1432 Ås Norway, Norway / National Hospital, Section for Gene Therapy, N-0027 Oslo, Norway.
    Nestestog, Ragnhild
    Plant Molecular Biology Laboratory, Department of Plant and Environmental Sciences, University of Life Sciences, PO Box 5003, N-1432 Ås Norway, Norway.
    Grini, Paul E.
    Department of Molecular Biosciences, University of Oslo, Oslo, PO Box 1041 Blindern, N-0316 Oslo, Norway.
    Skrbo, Nirma
    Department of Molecular Biosciences, University of Oslo, Oslo, PO Box 1041 Blindern, N-0316 Oslo, Norway.
    Berg, Anita
    Department of Molecular Biosciences, University of Oslo, Oslo, PO Box 1041 Blindern, N-0316 Oslo, Norway.
    Salehian, Zhian
    Plant Molecular Biology Laboratory, Department of Plant and Environmental Sciences, University of Life Sciences, PO Box 5003, N-1432 Ås Norway, Norway.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för kommunikation och information.
    Aalen, Reidunn B.
    Department of Molecular Biosciences, University of Oslo, Oslo, PO Box 1041 Blindern, N-0316 Oslo, Norway.
    Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: Reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5′ end of genes2005Inngår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 56, nr 419, s. 2495-2505Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Random insertions of promoterless reporter genes in genomes are a common tool for identifying marker lines with tissue-specific expression patterns. Such lines are assumed to reflect the activity of endogenous promoters and should facilitate the cloning of genes expressed in the corresponding tissues. To identify genes active in seed organs, plant DNA flanking T-DNA insertions (T-DNAs) have been cloned in 16 Arabidopsis thaliana GUS-reporter lines. T-DNAs were found in proximal promoter regions, 5' UTR or intron with GUS in the same (sense) orientation as the tagged gene, but contrary to expectations also in inverted orientation in the 5' end of genes or in intergenic regions. RT-PCR, northern analysis, and data on expression patterns of tagged genes, compared with the expression pattern of the reporter lines, suggest that the expression pattern of a reporter gene will reflect the pattern of a tagged gene when inserted in sense orientation in the 5' UTR or intron. When inserted in the promoter region, the reporter-gene expression patterns may be restricted compared with the endogenous gene. Among the trapped genes, the previously described nitrate transporter gene AtNRT1.1, the cyclophilin gene ROC3, and the histone deacetylase gene AtHD2C were found. Reporter-gene expression when positioned in antisense orientation, for example, in the SLEEPY1 gene, is indicative of antisense expression of the tagged gene. For T-DNAs found in intergenic regions, it is suggested that the reporter gene is transcribed from cryptic promoters or promoters of as yet unannotated genes.

  • 52.
    Stangeland, Biljana
    et al.
    University of Oslo.
    Rosenhave, E. Maryann
    University of Oslo.
    Winge, Per
    Norwegian University of Science and Technology.
    Berg, Anita
    University of Oslo.
    Amundsen, Silja S.
    University of Oslo.
    Karabeg, Mirela
    University of Oslo.
    Mandal, Abul
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Bones, Atle M.
    Norwegian University of Science and Technology.
    Grini, Paul E.
    University of Oslo.
    Aalen, Reidunn B.
    University of Oslo.
    AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana2009Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 136, nr 1, s. 110-126Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Arabidopsis thaliana accession C24 is a vernalization-responsive, moderately late flowering ecotype. We report that a mutation in AtMBD8, which encodes a protein with a putative Methyl-CpG-Binding Domain (MBD), in C24 background, results in a delay in flowering time during both long and short days. The atmbd8-1 mutant responded to vernalization as wild type (wt) plants. Consistent with a role in modulation of flowering time, an AtMBD8::GUS-reporter construct was expressed in the shoot meristem region and developing leaves. Full-genome transcriptional profiling revealed very few changes in gene expression between atmbd8-1 and wt plants. The expression level of FLC, the major repressor of transition to flowering, was unchanged in atmbd8-1, and in accordance with that, genes upstream of FLC were unaffected by the mutation. The expression level of CONSTANS, involved in photoperiodic control of flowering, was very similar in atmbd8-1 and wt plants. In contrast, the major promoters of flowering, FT, and SOC1, were both downregulated. As FT is a regulator of SOC1, we conclude that AtMBD8 is a novel promotor of flowering that acts upstream of FT in the C24 accession. In contrast to atmbd8-1, the Colombia (Col) SALK T-DNA insertion line, atmbd8-2, did not display a delayed transition to flowering. Transcriptional profiling revealed that a substantial number of genes were differentially expressed between C24 and Col wt seedlings. Several of these genes are also differentially expressed in late flowering mutants. We suggest that these differences contribute to the contrasting effect of a mutation in AtMBD8 in the two ecotypes.

  • 53.
    Sutkowska, Agnieszka
    et al.
    University of Agriculture in Krakow, Poland.
    Pasierbinski, Andrzej
    University of Silesia in Katowice, Poland.
    Warzecha, Tomasz
    University of Agriculture in Krakow, Poland.
    Mandal, Abul
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Mitka, Jozef
    Jagiellonian University in Krakow, Poland.
    Refugial pattern of Bromus erectus in Central Europe based on ISSR fingerprinting: Phylogeography of Bromus erectus in Central Europe2013Inngår i: Acta Biologica Cracoviensia. Series Botanica, ISSN 0001-5296, E-ISSN 1898-0295, Vol. 55, nr 2, s. 107-119Artikkel i tidsskrift (Fagfellevurdert)
    Fulltekst (pdf)
    SSutkowska et al-2013
  • 54.
    Svensson, Maria
    et al.
    Högskolan i Skövde, Institutionen för vård och natur.
    Lundh, Dan
    Högskolan i Skövde, Institutionen för kommunikation och information.
    Bergman, Per
    Department of Plant Biology and Forest Genetics, SLU, SE-750 07 Uppsala, Sweden.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för vård och natur.
    Characterisation of a T-DNA-tagged gene of Arabidopsis thaliana that regulates gibberellin metabolism and flowering time2005Inngår i: Functional Plant Biology, ISSN 1445-4408, E-ISSN 1445-4416, Vol. 32, nr 10, s. 923-932Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A gene (At4g20010) involved in regulating flowering time in Arabidopsis thaliana (L.) Heynh. was identified by promoter trap T-DNA tagging. Plants containing a T-DNA insert in the 3′-UTR of At4g20010 flowered later under both long- and short-day conditions compared with control plants. Histochemical assays of the mutant plants showed that the promoterless gus gene is expressed predominantly in the shoot apex, but it is also expressed in root tips, stem nodes and in the abscission zone of developing siliques. Measurement of endogenous gibberellin (GA) showed that bioactive GA4 levels in mutant plants were reduced compared with wild type (WT) plants. Like other known mutants defective in GA biosynthesis, the late-flowering phenotype observed in our T-DNA-tagged line could be largely repressed by application of exogenous GA3. The T-DNA-tagged gene At4g20010 encodes a previously uncharacterised protein belonging to the DUF731 family. Sequence analysis showed similarity to a single-stranded binding domain and to an RNA-binding protein of Chlamydomonas reinhardtii. Considering the above results (sequence similarity, mutant phenotype and level of endogenous GA), we propose that At4g20010 is an RNA-binding protein involved in regulating GA biosynthesis, possibly at the post-transcriptional level.

  • 55.
    Svensson, Maria
    et al.
    Högskolan i Skövde, Institutionen för vård och natur.
    Lundh, Dan
    Högskolan i Skövde, Institutionen för kommunikation och information.
    Ejdebäck, Mikael
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för vård och natur.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för vård och natur.
    Functional prediction of a T-DNA tagged gene of Arabidopsis thalianaby in silico analysis2004Inngår i: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 10, nr 2, s. 130-138Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have employed a gene-knockout approach using T-DNA tagging and in vivo gene fusion in Arabidopsis thaliana for identification and isolation of specific plant genes. Screening of about 3,000 T-DNA tagged lines resulted in identification of a mutant line (no. 197) exhibiting a significant delay in flowering. From this line a 600-bp plant DNA fragment downstream of the left T-DNA junction was cloned by inverse PCR. BLAST searching in the A. thaliana genomic database indicated a putative gene, frf (flowering regulating factor), with unknown function downstream of the T-DNA insert. Bioinformatic tools were used to predict possible protein structure and function. The protein structure predicted by fold recognition indicates that frf is a transcriptional regulator, a ligand-binding receptor responsive to steroids and hormones. Analyzing the predicted results and the phenotype of the T-DNA tagged plant we hypothesized that FRF might be involved in hormone response in A. thaliana. For verification of this hypothesis we exposed the plants of line no. 197 to gibberellic acid (GA3), a potential growth regulator in higher plants. This treatment resulted in an earlier onset of flowering, almost similar to that in wild type control plants.

  • 56.
    Warzecha, Tomasz
    et al.
    University of Agriculture, Kraków, Poland.
    Lundh, Dan
    Högskolan i Skövde, Institutionen för vård och natur. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för vård och natur. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Effect of Fusarium culmorum infection on survivability of a T-DNA tagged mutant of Arabidopsis thaliana harboring a mutation in the peptide transporter gene At5g460502011Inngår i: Biotechnologia: Journal of Biotechnology, Computational Biology and Bionanotechnology, ISSN 0860-7796, Vol. 92, nr 1, s. 77-84Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Previously, we have reported a T-DNA tagged mutant (TAG_009) of Arabidopsis thaliana exhibiting a significant sensitivity to biotic stresses. We have also cloned and analyzed the tagged gene At5g46050. Based on bioinformatic and molecular characterization, we proposed that At5g46050 is involved in the transport of peptides participating in plant defense against biotic stresses. To provide further evidence for supporting our proposal, this time we exposed this mutant to Fusarium culmorum, a potential fungal pathogen. Besides TAG_009 line, in our investigations we included two SALK insertion mutants (SALK_003119 and SALK_145209), two wild-type ecotypes (WT_C24 and WT_Col-0) and an additional T-DNA tagged mutant (TAG_197-6) of A. thaliana. We have found that the highest degree of leaf damage was exhibited by TAG_009 line (damage score 4.37), whereas the lowest was observed in WT_Col-0 ecotype (damage score 3.43). The highest rate of mortality after eight weeks of inoculation with F. culmorum was also observed in TAG_009 line (85.24%), while the lowest was in WT_Col-0 line (37.22%). We have also found that plants of SALK_145209 line, despite being infected with Fusarium, produced the highest number of leaves (average 14.17 leaves per plant), whereas the lowest number of leaves was produced by plants of TAG_197-6 line ( average 9.5 leaves per plant). Statistical analyses showed that the differences between the T-DNA tagged line TAG_009 and WT_Col-0 were significant, whereas in comparison with wild-type control plants WT_C24, they were insignificant. Based on these results, we can conclude that the gene we have tagged by using T-DNA-mediated in vivo gene fusion is indeed involved in the plant defense against Fusarium infection.

  • 57.
    Yewale, Priti Prabhakar
    et al.
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Lokhande, Kiran Bharat
    Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Sridhar, Aishwarya
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Vaishnav, Monika
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Khan, Faisal Ahmad
    The Life Science Centre-Biology, School of Science and Technology, Örebro University, Sweden.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Swamy, Kakumani Venkateswara
    Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Jass, Jana
    The Life Science Centre-Biology, School of Science and Technology, Örebro University, Sweden.
    Nawani, Neelu
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Molecular profiling of multidrug-resistant river water isolates: insights into resistance mechanism and potential inhibitors2019Inngår i: Environmental science and pollution research international, ISSN 0944-1344, E-ISSN 1614-7499Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Polluted waters are an important reservoir for antibiotic resistance genes and multidrug-resistant bacteria. This report describes the microbial community, antibiotic resistance genes, and the genetic profile of extended spectrum β-lactamase strains isolated from rivers at, Pune, India. ESBL-producing bacteria isolated from diverse river water catchments running through Pune City were characterized for their antibiotic resistance. The microbial community and types of genes which confer antibiotic resistance were identified followed by the isolation of antibiotic-resistant bacteria on selective media and their genome analysis. Four representative isolates were sequenced using next generation sequencing for genomic analysis. They were identified as Pseudomonas aeruginosa, Escherichia coli, and two isolates were Enterobacter cloacae. The genes associated with the multidrug efflux pumps, such as tolC, macA, macB, adeL, and rosB, were detected in the isolates. As MacAB-TolC is an ABC type efflux pump responsible for conferring resistance in bacteria to several antibiotics, potential efflux pump inhibitors were identified by molecular docking. The homology model of their MacB protein with that from Escherichia coli K12 demonstrated structural changes in different motifs of MacB. Molecular docking of reported efflux pump inhibitors revealed the highest binding affinity of compound MC207-110 against MacB. It also details the potential efflux pump inhibitors that can serve as possible drug targets in drug development and discovery. 

  • 58.
    Yewale, Priti Prabhakar
    et al.
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Maharashtra, Pune, India.
    Rahman, Aminur
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Nahar, Noor
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Saha, Anandakumar
    Department of Zoology, University of Rajshahi, Rajshahi, Bangladesh.
    Jass, Jana
    The Life Science Center, The School of Science and Technology, Örebro University, Örebro, Sweden.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Nawani, Neelu N.
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India.
    Sources of Metal Pollution, Global Status, and Conventional Bioremediation Practices2017Inngår i: Handbook of Metal–Microbe Interactions and Bioremediation / [ed] Surajit Das, Hirak Ranjan Dash, Boca Raton, FL: CRC Press, 2017, s. 25-40Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Pollution control has become a priority task for global regulatory authorities. The framing of regulations, guidelines, and implementation of pollution awareness and control programs has begun at a massive scale. Heavy metals that are one of the most challenging pollutants that affect humans, animals, plants, and the ecosystem health. The sources of different metals and their toxicities are described. Current approaches in bioremediation are addressed along with the challenges posed by them. Furthermore, recent developments in biotechnology that offer novel ways to recover metals from contaminated sites are discussed.

12 51 - 58 of 58
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