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  • 1.
    Ali, Nada
    University of Skövde, School of Bioscience.
    Stress response in cancer cell lines2023Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Globally, the cases of cancer have been on the rise. This has led to increasing research to find a lasting solution to carcinogenesis. The increase in cancer cases can be due to a change in people’s lifestyles, such as diet and exercise routines which have changed for the worse. In most farms, chemicals as pesticides are added to plants to fasten their growth. These chemicals are carcinogenic, contributing to the increased number of cancer cases worldwide.

    The objective of this research was to observe the cell response of brain, pancreatic, and breast cancer cells to different cortisol levels/concentrations. The three cell lines of interest in this research and present in the mentioned types of cancer are T-47D, PANC-1, and T98G. Their dynamics and roles are identified in this study. Cortisol excretion concentrations during stress and cancer growth are also monitored and compared. Additionally, the study solves the unpredictability of the impacts of stress on the three cancer types.

    The three experimental setups in this study were as follows: 1. Breast cancer cells, obtained from a 54 year old woman with metastatic carcinoma. 2. Brain cancer cells, obtained from a 61 year old female with neuroblastoma. 3. Pancreatic cancer cells, obtained from a 56 year old male with metastatic carcinoma. The cells in the above setups were treated with cortisol in order to see what effect this induced stress has on cell growth.

    The findings of the study concluded higher cortisol concentration increased cancer growth and spread within the body. This was that all three cancer cell types saw an increased effect of cortisol at either 24 hours or 48 hours at a specific concentration, which highlights that cortisol has an important role to play in cancer cells viability.

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  • 2.
    Chowdhury, Manjushree
    et al.
    Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh.
    Mostafa, M. G.
    Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh.
    Biswas, Tapan Kumar
    Department of Chemistry, University of Rajshahi, Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Saha, Ananda Kumar
    Department of Zoology, University of Rajshahi, Rajshahi, Bangladesh.
    Characterization of the effluents from leather processing industries2015In: Environmental Processes, ISSN 2198-7491, Vol. 2, no 1, p. 173-187Article in journal (Refereed)
  • 3.
    Das, Umi
    et al.
    Molecular Plant Physiology Laboratory, Department of Botany, University of Rajshahi, Bangladesh.
    Haque, A. F. M. Mohabubul
    Molecular Plant Physiology Laboratory, Department of Botany, University of Rajshahi, Bangladesh.
    Bari, Md Azizul
    Adina Fazlul Haque Government College, Chapainawabganj, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Kabir, Ahmad Humayan
    Molecular Plant Physiology Laboratory, Department of Botany, University of Rajshahi, Bangladesh.
    Computational characterization and expression profile of MTP1 gene associated with zinc homeostasis across dicot plant species2021In: Gene Reports, ISSN 2452-0144, Vol. 23, p. 1-13, article id 101073Article in journal (Refereed)
    Abstract [en]

    This study characterizes different MTP1 (metal tolerance protein)/ZAT (zinc transporter) homologs involved in zinc (Zn) homeostasis in plants. BLAST analysis of AtMTP1 protein against 15 plant species showed 21 MTP1 homologs. These MTP1 protein homologs generally contain ~400 residues, six transmembrane helices and cation transmembrane transporter activity (GO:0008324), which can be utilized in predicting Zn uptake and tolerance mechanisms. These MTP1 genes having 1 exon are located on chromosomes 2, 7, and 14. Motifs contain conserved sequences of 41–50 residues belonging to the cation efflux family, which may help target binding sites and transcription factors. Further, AtMTP1 shows close similarities with Glycine max and Medicago trunculata. Interactome analysis suggests the association of AtMTP1 with cadmium/zinc-transporting ATPase and ZIP metal ion transporter. The AtMTP1 network is predominantly connected to cadmium/zinc-transporting ATPase (heavy metal ATPase 2, HMA2; heavy metal ATPase 3, HMA3; heavy metal ATPase 4, HMA4), cation efflux protein (MTP11), and metal tolerance protein C3 (AT4G58060). The Genevestigator predicts the high expression potential of AtMTP1 in the apical root during senescence, seedling, and bolting stages in an association with 11 co-expressed genes, mainly linked to estradiol toxicity and heat stress. Besides, AtMTP1 protein homologs possess conserved N-glyco motifs and physicochemical properties. The similarity and interactions of AtMTP1 gene with other genes suggest that Zn homeostasis in plants is associated with the regulation of different genes. These findings may advance our understanding to further develop plants capable of maintaining Zn homeostasis under adverse conditions. © 2021 Elsevier Inc.

  • 4.
    Desale, Prithviraj
    et al.
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Mumbai-Pune Expressway, Survey No. 87/88, Tathawade, Pune 411033, India.
    Prakash, Divya
    Department of Microbiology, University of Pune, Pune 41107. India.
    Keyur, Patel
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Mumbai-Pune Expressway, Survey No. 87/88, Tathawade, Pune 411033, India.
    Rupali, Aursang
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Mumbai-Pune Expressway, Survey No. 87/88, Tathawade, Pune 411033, India.
    Nawani, Neelu
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Mumbai-Pune Expressway, Survey No. 87/88, Tathawade, Pune 411033, India.
    Kapadnis, Balasaheb
    Department of Microbiology, University of Pune, Pune 41107. India.
    Khetmalas, Madhukar
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Mumbai-Pune Expressway, Survey No. 87/88, Tathawade, Pune 411033, India.
    Mandal, Abul
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Biosorption of Heavy Metals by Actinomycetes for Treatment of Industrial Effluents2012In: / [ed] Buhri Arifin, Siti Nur`Afifah Jaafar, Sayed Mohamed Zain S. Hasan, Anuar Hassan, H. M. Edi Armanto, Chuah Tse Seng, Wan Zaliha Wan Sembok, Shahreza Md Sheriff, Suparjo Noordin Mokhtar, Fazlil Ilahi Abdul Wahab, Hayati Mohd Yusof, Adzemi Mat. Arshad, Universiti Malaysia Terengganu , 2012, p. 389-393Conference paper (Refereed)
    Abstract [en]

    Rapid industrialization usually is the cause of increase in pollutants in the natural river bodies. This pollution is attributed to lack of improper treatment and inadequate disposal mechanisms of the waste generated thereof. The aim of present investigation was to screen actinomycetes for their ability to adsorb heavy metals. Actinomycetes belong to most diverse group of filamentous prokaryotes with ubiquitous presence in different ecological niches. This ubiquity is due to their ability to degrade almost any type of polymer and to use several compounds as carbon sources. Nearly 200 actinomycetes from different niches like fresh water, soda lake, geothermal springs, acid soils, etc from different locations in India were screened for ability to grow in presence of 1 to 5 mM of heavy metals like Cd, Hg, Pb, Ni, Sr, Fe, Mo, Zn and Mn. Most of the strains tolerant to heavy metals belonged to the genus Streptomyces spp. Five strains could grow in presence of 5 mM Cd2+, 4 strains in presence of 0.1 mM Hg2+, 18 strains in presence of 5 mM Pb2+, 21 strains in presence of 5 mM Ni2+, whereas 34 strains grew in presence of 5 mM Fe2+. One of the most promising strain was studied for its ability to absorb cadmium where 2x1011 cells or spores could adsorb 0.32 mM to 0.33 mM of cadmium. Spores and vegetative cells showed nearly similar level of adsorbtion ability. This strain can be very useful in developing a bioreactor for the adsorption of heavy metals from industrial effluents containing cadmium.

  • 5.
    Eriksson, Katarina
    et al.
    Alands Cent Sjukhus, Dept Obstet & Gynecol, Mariehamn, Finland / Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden .
    Larsson, Per-Göran
    University of Skövde, School of Life Sciences.
    Nilsson, Maud
    Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden .
    Forsum, Urban
    Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden .
    Vaginal retention of locally administered clindamycin2011In: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 119, no 6, p. 373-376Article in journal (Refereed)
    Abstract [en]

    Since bacterial vaginosis (BV) is characterized by a lack of, or very few, lactobacilli and high numbers of small, mostly anaerobic bacteria, an obvious treatment modality would be eradication of the BV-associated bacterial flora followed by reintroduction of lactobacilli vaginally. As probiotic treatment with lactobacilli is one tool for improving the cure rate when treating BV, it is necessary to know the length of time after treatment that clindamycin can be found in the vagina and if this could interfere with the growth of the probiotic lactobacilli. We evaluated the vaginal concentration of clindamycin in 12 women for 8 days to obtain data on the concentration of clindamycin in the vagina after intravaginal treatment with the drug. The participants were examined five times between two menstrual periods: before treatment, the day after treatment was finished, and 3, 5 and 8 days post-treatment. The first day post-treatment clindamycin 0.46 x 10-3 to 8.4 x 10-3 g/g vaginal fluid (median 2.87 x 10-3) was found. Thereafter, the concentration of clindamycin decreased rapidly. In 10 patients clindamycin was found after 3 days. A very low concentration was still present 5 days after treatment in four patients. After 8 days no clindamycin was found. Clindamycin is rapidly eliminated from the vagina, within 3-8 days, after local administration. Our results indicate that treatment with probiotic lactobacilli could be problematic if carried out within 5 days after cessation of clindamycin treatment.

  • 6.
    Fagerlind, Magnus G.
    et al.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Webb, Jeremy S.
    Univ Southampton, Sch Biol Sci, Southampton SO16 7PX, Hants, England .
    Barraud, Nicolas
    Univ New S Wales, Ctr Marine Bioinnovat, Sydney, NSW 2052, Australia / Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia .
    McDougald, Diane
    Univ New S Wales, Ctr Marine Bioinnovat, Sydney, NSW 2052, Australia / Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia / Nanyang Technol Univ, Adv Environm Biotechnol Ctr, Singapore 639798, Singapore .
    Jansson, Andreas
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Nilsson, Patric
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Harlen, Mikael
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Kjelleberg, Staffan
    Univ New S Wales, Ctr Marine Bioinnovat, Sydney, NSW 2052, Australia / Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia / Nanyang Technol Univ, Singapore Ctr Environm Life Sci Engn, Singapore 639798, Singapore .
    Rice, Scott A.
    Univ New S Wales, Ctr Marine Bioinnovat, Sydney, NSW 2052, Australia / Univ New S Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia / Nanyang Technol Univ, Singapore Ctr Environm Life Sci Engn, Singapore 639798, Singapore .
    Dynamic modelling of cell death during biofilm development2012In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 295, p. 23-36Article in journal (Refereed)
    Abstract [en]

    Biofilms are currently recognised as the predominant bacterial life-style and it has been suggested that biofilm development is influenced by a number of different processes such as adhesion, detachment, mass transport, quorum sensing, cell death and active dispersal. One of the least understood processes and its effects on biofilm development is cell death. However, experimental studies suggest that bacterial death is an important process during biofilm development and many studies show a relationship between cell death and dispersal in microbial biofilms. We present a model of the process of cell death during biofilm development, with a particular focus on the spatial localisation of cell death or cell damage. Three rules governing cell death or cell damage were evaluated which compared the effects of starvation, damage accumulation, and viability during biofilm development and were also used to design laboratory based experiments to test the model. Results from model simulations show that actively growing biofilms develop steep nutrient gradients within the interior of the biofilm that affect neighbouring microcolonies resulting in cell death and detachment. Two of the rules indicated that high substrate concentrations lead to accelerated cell death, in contrast to the third rule, based on the accumulation of damage, which predicted earlier cell death for biofilms grown with low substrate concentrations. Comparison of the modelling results with experimental results suggests that cell death is favoured under low nutrient conditions and that the accumulation of damage may be the main cause of cell death during biofilm development. (C) 2011 Elsevier Ltd. All rights reserved.

  • 7.
    Ferreira de Vilcinskas, Robherta
    University of Skövde, School of Bioscience.
    Identification of Lactobacillus species in honey using 16S rRNA gene sequencing2022Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Honey is a natural product composed of numeral substances and microorganisms. Although honey presents physicochemical properties that confer antimicrobial characteristics, certain microorganisms are still able to survive and multiply in honey. Some of these microorganisms are important to human health, such as Lactobacillus bacteria, which can be used as probiotic to improve human gastrointestinal condition. However, there is still a lack of knowledge about the microorganisms found in honey, and further research is necessary to better identify and understand these microorganisms. The aim of this study was to detect and identify Lactobacillus species from honey by sequencing the 16S ribosomal RNA gene with the universal primers 27F and 1492R. This was partly obtained by searching for Lactobacillus spp. directly in pure honey and after growing the unknown viable Lactobacillus spp. from honey in selective media. The microorganisms were isolated by centrifugation, had their DNA extracted, and only the bacterial 16S rRNA gene was amplified using Polymerase Chain Reaction and sequenced using the Oxford MinION Nanopore sequencing technology. EPI2ME, Oxford Nanopore Technology data analysis platform, was used to identify the bacteria. Results showed the presence of numeral Lactobacillus species in honey such as L. melliventris, L. mellifer, L. mellis, and L. helsinbgborgen, but in very low amounts. The analysis of honey samples was quite difficult. Low PCR product yield during the entire study, microscopic visualization and microbial analysis using fungicides supported the presence of fungi. In conclusion, a diversity of Lactobacillus spp. can be found in honey but in low quantities.

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  • 8.
    Futo, Momir
    et al.
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
    Opašić, Luka
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia / Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.
    Koska, Sara
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
    Čorak, Nina
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
    Široki, Tin
    Faculty of Electrical Engineering and Computing, University of Zagreb, Croatia.
    Ravikumar, Vaishnavi
    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
    Thorsell, Annika
    Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Lenuzzi, Masa
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia / Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
    Kifer, Domagoj
    Faculty of Pharmacy and Biochemistry, University of Zagreb, Croatia.
    Domazet-Lošo, Mirjana
    Faculty of Electrical Engineering and Computing, University of Zagreb, Croatia.
    Vlahoviček, Kristian
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Croatia.
    Mijakovic, Ivan
    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark / Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Domazet-Lošo, Tomislav
    Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia / Catholic University of Croatia, Zagreb, Croatia.
    Embryo-Like Features in Developing Bacillus subtilis Biofilms2021In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 38, no 1, p. 31-47Article in journal (Refereed)
    Abstract [en]

    Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.

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  • 9.
    Junnarkar, Manisha
    et al.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Pawar, Sarika
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Gaikwad, Swapnil
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Jass, Jana
    The Life Science Centre, School of Science and Technology, Örebro University, Örebro, Sweden.
    Nawani, Neelu
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Tathawade, Maharashtra, India.
    Probiotic potential of lactic acid bacteria from fresh vegetables: Application in food preservation2019In: Indian Journal of Experimental Biology, ISSN 0019-5189, E-ISSN 0975-1009, Vol. 57, p. 825-838Article in journal (Refereed)
    Abstract [en]

    Fresh vegetables are potential source of lactic acid bacteria (LAB). In the present study, LAB were isolated from the fresh vegetables from Pune region. Total 266 LAB were isolated from the edible parts of fresh vegetables viz. cauliflower, gherkins, cluster beans, fenugreek, cow pea, bitter gourd, french beans, tomato, ridged gourd, cucumber and bottle gourd. On phenotypic and molecular characterization predominant genera obtained were Lactobacillus, Enterococcus and Weissella. Twenty one isolates exhibited tolerance to bile salt, acidic pH and pancreatin. Cellular extracts of several isolates with ability to survive in artificial intestinal condition additionally showed antioxidant potential and cell free supernatants xhibited antibacterial potential against selected plant and human pathogens. Bacteriocin and bacteriocin like substances (BLS) substances secreted by these isolates can be used for food preservation.

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  • 10.
    Kokkonen, Alexander
    University of Skövde, School of Bioscience.
    Evaluation of next-generation sequencing as a tool for determining the presence of pathogens in clinical samples2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Metagenomic sequencing is an increasingly popular way of determining microbial diversity from environmental and clinical samples. By specifically targeting the 16S rRNA gene found in all bacteria, classifications of pathogens can be determined based on the variable and conserved regions found in the gene. Metagenomic sequencing can therefore highlight the vast difference in microbiological diversity between culture-dependent and culture-independent methods. Today, this has expanded into various next-generation sequencing platforms which can provide massively parallel sequencing of the target fragment. One of these platforms is Ion-torrent, which can be utilized for targeting the 16S rRNA gene and with the help of bioinformatics pipelines be able to classify pathogens using the bacteria’s own variable and conserved regions. The overall aim of the present work is to evaluate the clinical use of Ion-torrent 16S ribosomal RNA sequencing for determining pathogenic species from clinical samples, but also to set up a pipeline for clinical practice. Optimal DNA-extraction and quantification methods were determined towards each evaluated sample-type and DNA-eluates were sent for 16S rRNA Sanger and Next-generation sequencing. The result indicated that the next-generation sequencing shows a concordance in results towards the culturing-based method, but also the importance of experimental design and effective quality trimming of the NGS data. The conclusion of the project is that the Ion-torrent pipeline provided by the Public Health Agency of Sweden shows great promise in determining pathogens from clinical samples. However, there is still a lot of validation and standardisations needed for the successful implementation into a clinical setting.

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  • 11.
    Liu, Oscar H.
    University of Skövde, School of Bioscience.
    RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis2014Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Helicobacter pylori infects more than half of the world's population, and is known to be involved in several diseases including gastric cancer. Its close interactions with the stomach and host immune system serves as a good model to study the co-adaptation and co-evolution of the organisms in the stomach micro-environment. In this project, we utilized RNA-seq and data analysis tools to investigate differentially expressed genes by H. pylori in patients at different stages of early gastric cancer development. We also investigated the abundance and diversity of bacterial genera other than H. pylori, and looked for correlations with H. pylori presence and number. For differential gene expression of H. pylori, one gene was differentially expressed between samples of corpus atrophy without metaplasia vs. samples of antrum gastritis, and eight genes were found to be differentially expressed between samples of corpus atrophy with metaplasia vs. samples with pan-gastritis. When samples were clustered into different groups based on the expression data, 52 genes (shared or unique to the specific comparison groups) were found to be differentially expressed, but no apparent patterns were observed that could be explained by medical or sample collection data. For bacterial diversity and abundances, we found several genera colonizing the stomach, of which some have been previously identified. While most of these bacteria colonize regardless of the presence of H. pylori, the abundance of three genera, Wolinella, Campylobacter, and Veillonella, seem to be correlated with the presence of H. pylori.

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    Liu, Oscar H.. RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis
  • 12.
    Liu, Oscar H.
    University of Skövde, School of Bioscience.
    RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis2014Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Helicobacter pylori infects more than half of the world's population, and is known to be involved in several diseases including gastric cancer. Its close interactions with the stomach and host immune system serves as a good model to study the co-adaptation and co-evolution of the organisms in the stomach micro-environment. In this project, we utilized RNA-seq and data analysis tools to investigate differentially expressed genes by H. pylori in patients at different stages of early gastric cancer development. We also investigated the abundance and diversity of bacterial genera other than H. pylori, and looked for correlations with H. pylori presence and number. For differential gene expression of H. pylori, one gene was differentially expressed between samples of corpus atrophy without metaplasia vs. samples of antrum gastritis, and eight genes were found to be differentially expressed between samples of corpus atrophy with metaplasia vs. samples with pan-gastritis. When samples were clustered into different groups based on the expression data, 52 genes (shared or unique to the specific comparison groups) were found to be differentially expressed, but no apparent patterns were observed that could be explained by medical or sample collection data. For bacterial diversity and abundances, we found several genera colonizing the stomach, of which some have been previously identified. While most of these bacteria colonize regardless of the presence of H. pylori, the abundance of three genera, Wolinella, Campylobacter, and Veillonella, seem to be correlated with the presence of H. pylori.

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    RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis
  • 13.
    Nawani, Neelu
    et al.
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Aigle, Bertrand
    Université de Lorraine, France ; INRA, Dynamique des Genomes et Adaptation Microbienne, France.
    Mandal, Abul
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Bodas, Manish
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Ghorbel, Sofiane
    Laboratoire de Génie Enzymatique et de Microbiologie, Ecole Nationale D’Ingénieurs de Sfax, Tunisia.
    Prakash, Divya
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, India.
    Actinomycetes: Role in Biotechnology and Medicine2013In: BioMed Research International, ISSN 2314-6133, E-ISSN 2314-6141, no 2013, p. 687190-Article in journal (Refereed)
    Abstract [en]

    Actinomycetes, one of the most diverse groups of filamentous bacteria, are well recognized for their metabolic versatility. The bioactive potential of these bacteria facilitates their survival even in distress and unfavourable ecological conditions. This special issue is dedicated to the importance of multitude of primary and secondary metabolites produced by actinomycetes. The importance of large repertory of enzymes from actinomycetes and their potential in replacing chemical catalysts is discussed.

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    Actinomycetes
  • 14.
    Nawani, Neelu
    et al.
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Present affiliation: Laboratory of Applied Microbiology, Faculty of Agriculture, Saga University, Japan.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Microbial biomass for sustainable remediation of wastewater2022In: Biomass, Biofuels, Biochemicals: Circular Bioeconomy: Technologies for Waste Remediation / [ed] Sunita Varjani; Ashok Pandey; Mohammad J. Taherzadeh; Huu Hao Ngo; R. D. Tyagi, Elsevier, 2022, p. 271-292Chapter in book (Refereed)
    Abstract [en]

    Microbial technologies play an extremely crucial role in wastewater treatment. In the last few decades, the focus was on wastewater treatment; however, with the consumption of already finite resources, this focus has now shifted to wastewater remediation and recycling. The latest technologies are more robust at wastewater treatment and the recovery of useful compounds from the wastewaters. This chapter compiles the latest technologies in which microbial/bacterial biomass was used for wastewater treatment and remediation. This chapter also gives a special focus on remediation of wastewaters contaminated with heavy metals, describing the basic technologies as well as smart technologies. Emphasis is given to circular bioeconomy and how it can be implemented in wastewater treatment. A circular model incorporating key areas such as point source detection of pollutants, characterization of wastewaters, choice of the remedial technology, and type of treatment is explained in the chapter.

  • 15.
    Nawani, Neelu
    et al.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Rahman, Aminur
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nahar, Noor
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Saha, Anandakumar
    Department of Zoology, University of Rajshahi, Bangladesh.
    Kapadnis, Balasaheb
    Department of Microbiology, Savitribai Phule University of Pune, Pune, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora2016In: Biologia, ISSN 0006-3088, E-ISSN 1336-9563, Vol. 71, no 5, p. 494-507Article in journal (Refereed)
    Abstract [en]

    This study illustrates the sporadic distribution of metals in fluvial systems flowing from catchments to urban settlements. This is a detailed study prognosticating the deteriorating quality of rivers at specific locations due to metal pollution. Heavy metals like cadmium, lead, nickel and mercury are prominent in industrial sector. Contour plots derived using spatial and temporal data could determine the focal point of metal pollution and its gradation. Metal values recorded were cadmium 157 mg/L, lead 47 mg/L, nickel 61 mg/L and mercury 0.56 mg/L. Prokaryote diversity was less in polluted water and it harboured metal tolerant bacteria, which were isolated from these polluted sites. Actinomycetes like Streptomyces and several other bacteria like Stenotrophomonas and Pseudomonas isolated from the polluted river sites exhibited changes in morphology in presence of heavy metals. This stress response offered remedial measures as Streptomyces were effective in biosorption of cadmium, nickel and lead and Stenotrophomonas and Pseudomonas were effective in the bioaccumulation of lead and cadmium. The amount of 89 mg of lead and 106 mg of nickel could be adsorbed on one gram of Streptomyces biomass-based biosorbent. Such biological remedies can be further explored to remove metals from polluted sites and from metal contaminated industrial or waste waters.

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    Biologia-1-2016
  • 16.
    Nematollahi Mahani, Seyed Alireza
    University of Skövde, School of Health and Education.
    Human placental trophoblast infection with rift valley fever virus and the cell cytokine response to infection2017Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Rift Valley Fever Virus (RVFV) is a Mosquito borne virus (Bunyaviridae family) associated withhemorrhagic fever and abortion in ruminants and humans. Geographic distribution of the virus has expanded to most countries in African continent and in 2001 to Arabian Peninsula resulting in repeated epidemic and epizootic events. With abortion being the hallmark of RVFV infection,Understanding RVFV infection in human placental tissue can provide better insight into disease pathobiology.

    In this study, three human trophoblast cell lines (A3, Jar & BeWo) were evaluated for permissiveness to RVFV infection. Furthermore, the viral capacity to spread by producing progeny viruses in trophoblasts was evaluated. The trophoblast response to infection was additionally assessed by measuring expression levels of important inflammatory cytokines in the cells (IL-1 β, IL-6, IL-8, IL-10, IL15, CSF-2, IFN-g, Fas-L). Finaly, two viral entrance mechanisms suggested for this virus were investigated in these cell models.

    Results suggested high permissiveness of studied trophoblasts cell lines to RVFV, leading to severe cytokine response (IL-8 and IL-1β in Jar and increase in CSF-2, IL-1β, IL-6 and IL-8 in A3 cell line). Since these cytokines are vital in embryonic regulation and development, the severe effect of infection could potentially be part of pathogenesis of virus-induced abortion. When viral entry routes were investigated, heparan sulfate proved to be the main cell entry membrane protein used by RVFV. However removal of all galactosylamintransferases resulted in higher infection rate suggesting presence of other entry mechanisms in absence of galactosylamin transferase. Considering these results and the nature of primary trophoblasts in resisting infection, it is important to evaluate if the primary trophoblasts show the same or similar pattern of sensitivity to RVFV infection with both wild type and mutated viral strains.These findings merit further investigations regarding pregnancy response to infection, vaccination and treatment.

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  • 17.
    Nushair, Ali Mohammad
    et al.
    University of Rajshahi, Bangladesh.
    Saha, Ananda Kumar
    University of Rajshahi, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Rahman, Md. Anisur
    University of Rajshahi, Bangladesh.
    Mohanta, Moni Krishno
    University of Rajshahi, Bangladesh.
    Hasan, Md. Ariful
    University of Rajshahi, Bangladesh.
    Haque, Md. Fazlul
    University of Rajshahi, Bangladesh.
    Rhizobium sp.CCNWYC119: a single strain highly effective as biofertilizer for three different peas (Pigeon pea, Sweet pea and Chick pea)2018In: Legume Research An International Journal, ISSN 0250-5371, Vol. 41, no 5, p. 771-777, article id LR-389Article in journal (Refereed)
    Abstract [en]

    Rhizobium spp. was isolated from root nodules of Pigeon pea (Cajanus cajan L.), Sweet pea (Lathyrus sativus L.), Chickpea (Cicer arietinum L.). The isolates ware rod shaped, aerobic, gram negative, motile and non-spore forming. Isolates were positive to Catalase, Citrate utilization, Urea hydrolysis, Congored, Nitrification, Oxidase, Triple sugar iron and MacConkey agar test. The isolates can ferment all nine sugars. Then, the isolates identified as Rhizobium spp. Depending on above results were subjected to 16S rRNA sequencing for further confirmation and identification. Surprisingly, theisolates were same strain or member of same cluster of Rhizobium and identified as Rhizobium sp.CCNWYC119 strain based on 16S rRNA sequence (98% similarity). Then, different parameters of soil quality enrichment and plant growth viz.plant height; weight of pods and seeds; number, fresh and dry weight of nodules were studied to test the efficacy of the isolate as biofertilizer. Here, inoculant of Rhizobium sp. isolated from Pigeon pea was used as biofertilizer. The results showed the significant increase of nodulation, enrichment of soil of rhizosphere, plant growth and yield for all three types of inoculated peas as compared with non-inoculated control peas indicating that the isolated strain could be used as a common efficient biofertilizer for Pigeon pea, Sweet pea and Chick pea. It was also found that the isolate grew optimally at temperature 28°C and pH 7.0.Moreover, the isolate was sensitive to the higher concentration of NaCl (>1%) and to antibiotics- Mecillinam, Ciprofloxacin,Cotrimoxazole, Pefloxacin, Ceftazidime and Tetracycline.

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  • 18.
    Olsson, Björn E.
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Korsakova, Ekaterina S.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Anan'ina, Lyudmila N.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Pyankova, Anna A.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Mavrodi, Olga V.
    Department of Biological Sciences, The University of Southern Mississippi, USA.
    Plotnikova, Elena G.
    Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Mavrodi, Dmitri V.
    Department of Biological Sciences, The University of Southern Mississippi, USA.
    Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia2017In: Standards in Genomic Sciences, E-ISSN 1944-3277, Vol. 12, no 39, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.

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  • 19.
    Rahman, Aminur
    University of Skövde, School of Bioscience.
    Microbial bioremediation and characterization of Arsenic resistant bacteria2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Arsenic is a toxic metalloid existing everywhere in the nature. It is toxic to most organisms and considered as human carcinogen. Arsenic contamination leads to severe health problems with diseases like damage of skin, lung, bladder, liver and kidney as well as central nervous system. As arsenic can be found everywhere in nature it may come in contact with food chain very easily through either water or cultivated crops. My thesis works include studies of bioremediation of arsenic by microorganisms. In this experiment the test organisms were collected from the Hazaribagh tanning industrial area of Dhaka, Bangladesh. The whole laboratory works were performed with two types of bacterial strains. Genomic DNA isolation and restriction digestion of genomic DNA, plasmid DNA isolation, Growth response to different concentrations of Arsenic, minimum inhibitory concentration (MIC), plasmid degradation procedures were carried out during this experiment. The MIC value for amoxicillin of these test organisms was 300 μg/ml and they are able to degrade 5 mM arsenite (AsIII) and 40 mM arsenate (AsV). Though the experiment was carried out with two bacterial strains but by observing all experimental data such as restriction digestion, growth response to the arsenic before and after treated with ethidium bromide and minimum inhibitory concentration it can be concluded that these two strains were not different. These bacteria are able to survive in high concentration of antibiotics and arsenic (AsV and AsIII). Loss of plasmid resulted no growth on media containing arsenic. These results support that plasmid contains important genes that are responsible for surviving bacteria in stress conditions.

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    Thesis Biomedicine
  • 20.
    Rahman, Aminur
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Örebro Universtitet.
    Nahar, Noor
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nawani, Neelu N.
    Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Tathawade, Pune, India.
    Jass, Jana
    The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden.
    Hossain, Khaled
    Department of Biochemistry & Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh.
    Alam Saud, Zahangir
    Department of Biochemistry & Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh.
    Saha, Ananda K.
    Department of Zoology, University of Rajshahi, Rajshahi, Bangladesh.
    Ghosh, Sibdas
    School of Arts and Science, Iona College, New Rochelle, New York, USA.
    Olsson, Björn
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Bioremediation of hexavalent chromium (VI) by a soil borne bacterium, Enterobacter cloacae B2-DHA2015In: Journal of Environmental Science and Health. Part A: Toxic/Hazardous Substances and Environmental Engineering, ISSN 1093-4529, E-ISSN 1532-4117, Vol. 50, no 11, p. 1136-1147Article in journal (Refereed)
    Abstract [en]

    Chromium and chromium containing compounds are discharged into the nature as waste from anthropogenic activities, such as industries, agriculture, forest farming, mining and metallurgy. Continued disposal of these compounds to the environment leads to development of various lethal diseases in both humans and animals. In this paper, we report a soil borne bacterium, B2-DHA that can be used as a vehicle to effectively remove chromium from the contaminated sources. B2-DHA is resistant to chromium with a MIC value of 1000 µg/mL potassium chromate. The bacterium has been identified as a Gram negative, Enterobacter cloacae based on biochemical characteristics and 16S rRNA gene analysis. TOF-SIMS and ICP-MS analyses confirmed intracellular accumulation of chromium and thus its removal from the contaminated liquid medium. Chromium accumulation in cells was 320 µg/g of cells dry biomass after 120 h exposure and thus it reduced the chromium concentration in the liquid medium by as much as 81%. Environmental scanning electron micrograph revealed the effect of metals on cellular morphology of the isolates. Altogether, our results indicate that B2-DHA has the potential to reduce chromium significantly to safe levels from the contaminated environments and suggest the potential use of this bacterium in reducing human exposure to chromium, hence avoiding poisoning.

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    Rahman et al., 2015
  • 21.
    Rahman, Aminur
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nahar, Noor
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nawani, Neelu N.
    Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Investigation on Arsenic-Accumulating and Arsenic-Transforming Bacteria for Potential Use in the Bioremediation of Arsenics2017In: Handbook of Metal-Microbe Interactions and Bioremediation / [ed] Surajit Das, Hirak Ranjan Dash, Boca Raton, FL: CRC Press, 2017, p. 509-519Chapter in book (Refereed)
    Abstract [en]

    In this chapter, arsenic-accumulating and arsenic- transformingbacterial strains that can be employed as a sourcefor cost-effective and eco-friendly bioremediation of arsenicsfrom contaminated environments have been reviewed. Thischapter demonstrates that many naturally occurring bacterialstrains like B1-CDA have the potential for reducing arseniccontent in contaminated sources to safe levels. Therefore,the socioeconomic impact of this kind of microorganisms ishighly significant for those countries, especially in the developingworld, where impoverished families and villages aremost impacted. Therefore, this discovery should be consideredto be the most significant factor in formulating nationalstrategies for effective poverty elimination. Besides humanarsenic contamination, these bacterial strains will also benefitlivestock and native animal species, and the outcome ofthese studies is vital not only for people in arsenic-affectedareas but also for human populations in other countries thathave credible health concerns as a consequence of arseniccontaminatedwater and foods.

  • 22.
    Rai, Vijeta
    University of Skövde, School of Bioscience.
    Screening of large collection of compounds for anti-human parainfluenza virus type-2 activity and evaluation of hit compounds2017Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Human parainfluenza virus type-2 (HPIV-2) is a highly contagious respiratory pathogen that can cause severe respiratory disease known as laryngotracheobronchitis or croup-like disease in children. No specific vaccine or an antiviral drug is currently approved for treatment of HPIV-2 infections. In this project, a library of 14400 diverse compounds had been screened for anti-HPIV-2 activities in cultures of African green monkey kidney cells. All compounds that inhibited the virus induced syncytium-forming activity in these cells were considered as hit compounds. Three hit compounds showed moderate anti-HPIV-2 activity characterized by the IC50 values of 20 µM and selectivity indices of approximately 5. This suggests that the antiviral activity of these compounds was due to targeting activities of cellular rather than viral components. Another hit compound, referred to as compound 5, showed anti-HPIV-2 activity that was manifested as a reduction of area of the virus-induced plaques in cells at not cytotoxic concentrations. Interestingly, this compound did not inhibit initial infection nor the virus production in infected cells as revealed by the time-of-addition assay. Moreover, it showed no direct the virus-inactivating (virucidal activity) against HPIV-2 particles. However, relatively short pre-treatment (4 hours) of the cells with compound 5 prior to the virus infection was sufficient for its plaque size-reducing activity suggesting that anti-HPIV-2 activity of compound 5 was due to targeting activities of cellular rather than viral components. Further studies are needed to elucidate the anti-HPIV-2 mechanism of activity of hit compounds identified in the present study.

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    vijeta rai
  • 23.
    Saha, Ananda Kumar
    et al.
    Department of Zoology, University of Rajshahi, Rajshahi-6205, Bangladesh.
    Sultana, Nahida
    Department of Zoology, University of Rajshahi, Rajshahi-6205, Bangladesh.
    Mohanta, Moni Krishno
    Department of Zoology, University of Rajshahi, Rajshahi-6205, Bangladesh.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Haque, Fazlul
    Identification and Characterization of Azo Dye Decolourizing Bacterial Strains, Alcaligenes faecalis E5.Cd and A. faecalis Fal.3 Isolated from Textile Effluents2017In: American Scientific Research Journal for Engineering, Technology, and Sciences (ASRJETS), ISSN 2313-4410, Vol. 31, no 1, p. 163-175Article in journal (Refereed)
    Abstract [en]

    The study was designed for isolation and characterization of azo dye decolourizing bacteria which is a prerequisite for developing a microorganism-facilitated treatment of polluting dyes. In this study nine types of bacteria which were able to decolourize three types of azo dyes (Blue H/C, Red 3B and Yellow 3R dye) were isolated from textile effluents collected from Gazipur industrial area in Bangladesh. Depending on 16S rDNA analysis, the most efficient decolourizing bacterium for the Blue H/C and the Red 3B dye was identified as Alcaligenesfaecalis strain E5.Cd while that for the Yellow 3R dye was identified as Alcaligenesfaecalis strain Fal.3. After characterization, both A. faecalis E5.Cdand A. faecalis Fal.3 were found to grow optimally at 35 0 C and at pH 7 and pH 8, respectively. Both of these strains were sensitive to all antibiotics studied except for Bacitracin. Also, both strains showed maximum decolourization activities after 96 hours incubation in MS media at pH 7 (up to 93%) and pH 8 (up to 94%), at 35 0 C temperature ( up to 91%), at 50 ppm initial dye concentration (up to 92%), at 20% inoculum size (up to 93%), and at supplementation of 1% co-substrate (up to 93%).

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  • 24.
    Salgaonkar, Neeta A.
    et al.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Thakare, Prasad M.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Junnarkar, Manisha V.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Kapadnis, Balasaheb P.
    Department of Microbiology, Savitribai Phule University of Pune, Pune, India.
    Mandal, Abul
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Eriksson, Cecilia
    University of Skövde, School of Health and Education. University of Skövde, Health and Education.
    Neelu, Nawani N.
    Microbial Diversity Research Centre, Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D Y Patil Vidyapeeth, Pune, India.
    Use of N,N-diacetylchitobiose in decreasing toxic effects of indoor air pollution by preventing oxidative DNA damage2016In: Biologia, ISSN 0006-3088, E-ISSN 1336-9563, Vol. 71, no 5, p. 505-515Article in journal (Refereed)
    Abstract [en]

    Indoor air pollution occurs due to hazardous pollutants, such as tobacco smoke, pesticides and carbon oxides, sulphur oxides and nitrogen oxides arising from combustion of biomass fuels. Exposure to these pollutants results in respiratory conditions like asthma, chronic obstructive pulmonary disease, lung cancer, pneumonia and other lower respiratory infections. Several of these infections are a result of inflammation and oxidative stress. Here we demonstrate the ability of N,N-diacetylchitobiose in preventing oxidative DNA damage in peripheral blood mononuclear cells exposed to biomass smoke extracts and cigarette smoke extract. The cytotoxic effect of these pollutants was determined by trypan blue exclusion assay in peripheral blood mononuclear cells, where cytotoxicity in decreasing order was  garette > wood > sawdust > cowdung. Cytotoxicity could be due to single- and double-strand breaks in the DNA as a result of oxidative stress. Comet assay measures the extent of DNA damage in the cells exposed to toxic agents. When mononuclear cells were treated with N,N-diacetylchitobiose and later exposed to smoke extracts, the extent of DNA damage decreased by 44.5% and 57.5% as compared to untreated cells. The protection offered by N,N-diacetylchitobiose towards oxidative DNA damage was at par with quercetin, a popular herbal medicine. Glutathione-S-transferase activity was determined in mononuclear cells exposed to smoke extracts, where oxidative stress in cells exposed to cigarette smoke extract was maximum. The present study demonstrates for the first time the ability of N,N -diacetylchitobiose to alleviate the harmful effects of indoor air pollutants.

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    Biologia-2-2016.pdf
  • 25.
    Shemirani, Mahnaz Irani
    et al.
    Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
    Tilevik, Diana
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Tilevik, Andreas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Jurcevic, Sanja
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Arnellos, Dimitrios
    1928 Diagnostics, Gothenburg, Sweden.
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis2023In: BMC Infectious Diseases, E-ISSN 1471-2334, Vol. 23, no 1, p. 39-, article id 39Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory.

    METHODS: Whole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement.

    RESULTS: There was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates.

    CONCLUSIONS: Altogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.

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  • 26.
    Shumkova, Ekaterina
    et al.
    A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia a/ Perm State University, Perm, Russia.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Kudryavtseva, Anna
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
    Plotnikova, Elena
    Perm State University, Perm, Russia / Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia.
    Draft Genome Sequence of Rhodococcus ruber Strain P25: an Active Polychlorinated Biphenyl Degrader2015In: Genome Announcements, E-ISSN 2169-8287, Vol. 3, no 5, article id e00990-15Article in journal (Refereed)
    Abstract [en]

    We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a soil polluted with halogenated aromatic compounds in the city of Perm, Russia. The strain degrades polychlorinated biphenyls and a broad range of aromatic compounds. It possesses genes that mediate the degradation of biphenyls/polychlorinated biphenyls, naphthalene, and monoaromatic compounds.

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    fulltext
  • 27.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Habitat requirements and distribution of wood- and bark inhabiting fungi on oak2006In: The oak: History, ecology, management and planning: Proceedings from a conference in Linköping, Sweden, 9-11 May, 2006 / [ed] Maria Engvall, Stockholm: Naturvårdsverket , 2006, p. 24-25Conference paper (Other academic)
  • 28.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Vedsvampar på ek - 12. Ekkrös: Exidia truncata2005In: Ekbladet: medlemsskrift för Ekfrämjandet, ISSN 0283-4839, Vol. 20, p. 35-37Article in journal (Other (popular science, discussion, etc.))
  • 29.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Vedsvampar på ek - 13. Limsvamp: Bulgaria inquinans2006In: Ekbladet: medlemsskrift för Ekfrämjandet, ISSN 0283-4839, Vol. 21, p. 11-14Article in journal (Other (popular science, discussion, etc.))
  • 30.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Vedsvampar på ek - 14. Rostöra2007In: Ekbladet: medlemsskrift för Ekfrämjandet, ISSN 0283-4839, Vol. 22, p. 33-36Article in journal (Other (popular science, discussion, etc.))
  • 31.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Vedsvampar på ek - 15. Askticka2008In: Ekbladet: medlemsskrift för Ekfrämjandet, ISSN 0283-4839, Vol. 23, p. 31-34Article in journal (Other (popular science, discussion, etc.))
  • 32.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Vedsvampar på ek - 16. Platticka2009In: Ekbladet, ISSN 0283-4839, Vol. 24, p. 30-35Article in journal (Other (popular science, discussion, etc.))
  • 33.
    Sunhede, Stellan
    University of Skövde, School of Life Sciences.
    Vedsvampar på ek: 11. Igelkottaggsvamp, Hericium erinaceum2004In: Ekbladet: medlemsskrift för Ekfrämjandet, ISSN 0283-4839, Vol. 19, no 1, p. 32-36Article in journal (Other (popular science, discussion, etc.))
  • 34.
    Sunhede, Stellan
    et al.
    University of Skövde, Department of Natural Sciences.
    Meiere, Diana
    The Faculty of Biology, Riga, Latvia.
    Vedsvampar på ek: 10. Ekskinn, Aleurodiscus disciformis2003In: Ekbladet: medlemsskrift för Ekfrämjandet, ISSN 0283-4839, Vol. 18, p. 27-30Article in journal (Other (popular science, discussion, etc.))
  • 35.
    Sunhede, Stellan
    et al.
    University of Skövde, Department of Natural Sciences.
    Vasiliauskas, Rimvydas
    Institutionen för skoglig mykologi och patologi, SLU, Uppsala.
    Hotade tickor på ek i Litauen2003In: Svensk botanisk tidskrift, ISSN 0039-646X, Vol. 97, no 5, p. 252-265Article in journal (Refereed)
    Abstract [en]

    Rare and endangered species of Aphyllophorales have been studied on Quercus robur in Lithuania. In total, 5455 trees and 742 stumps of oaks have been investigated in pure oak stands, mixed deciduous woods, mixed coniferous–deciduous woods, parks, and in open landscapes. Fungi in the herbarium BILAS (Vilnius) were examined.

    The ecology, distribution, and status of the following polypores are treated, viz Fistulina hepatica (Schaeff.: Fr.) With., Grifola frondosa (Dicks.: Fr) S.F.Gray, Hapalopilus croceus (Pers.: Fr.) Bond. & Sing, Inocutis dryophila (Berk) Fiasson & Niemelä, Inonotus dryadeus (Pers.: Fr.) Murr., Piptoporus quercinus (Fr.) Pilát, and Polyporus umbellatus (Pers.) ex Fr. Each species is briefly described and localities are listed in detail. All species, except F. hepatica and P. quercinus, are included in the Lithuanian Red List of fungi. We suggest these two species should be added to the list, and classified according to the IUCN categories Near Threatened (NT) and Endangered (EN), respectively.

    The importance of saving the right type of substrate and habitat for the actual species is stressed. Thick dead, standing or fallen trees, and old stumps should not be removed, as F. hepatica, G. frondosa, H. croceus, and P. quercinus may continue to fructify for many years on this type of wood. Suppression of old host trees, formerly growing in a more open environment, is a problem at many sites. A proper clearing around these oaks is necessary to keep the oaks alive as long as possible. The necessity of favouring younger oaks of different age classes in the stands is pointed out, as a continuous supply of thick host trees is needed to preserve the fungi.

    Hapalopilus croceus, one of Europe’s most endangered fungi, fructifies on old thick oaks, a substrate that becomes more and more rare. All Lithuanian host trees of H. croceus are proposed to be preserved (even when dead) together with a sufficient number of oaks in the surroundings. In Sweden, which is still one of the strongholds of H. croceus in Europe, the species is classified as Critically Endangered (CR) and since 2000 also protected.

    The following two oak sites in Lithuania are highly recommended to be preserved, more closely investigated, and managed for the future: Punios Šilas (squares 31, 32 & 38), Alytus district. In this very valuable locality, where many old and thick oaks are suppressed by surrounding younger trees, we found H. croceus (on 11 oaks), I. dryophila, F. hepatica, P. quercinus, and the red-listed beetle Osmoderma eremita (Scop.). “Kauno Ažuolynas” in Kaunas is a unique park with more than 800 mostly old, thick oaks, mixed with, e.g., Tilia. Here we observed F. hepatica, G. frondosa (on 11 oaks), H. croceus (on 8 oaks), and I. dryophila.

  • 36.
    Tilevik, Diana
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Fagerlind, Magnus
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Tilevik, Andreas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Ljungström, Lars
    Department of Infectious Diseases, Skaraborg Hospital, Skövde, Sweden.
    Johansson, Markus
    1928 Diagnostics, Arvid Hedvalls backe, Gothenburg, Sweden.
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment. Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skaraborg Hospital, Skövde.
    Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden2022In: Microbial Pathogenesis, ISSN 0882-4010, E-ISSN 1096-1208, Vol. 173, no Part A, article id 105836Article in journal (Refereed)
    Abstract [en]

    Extra-intestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a large number of human infections globally. The management of infections caused by ExPEC has been complicated by the emergence of antimicrobial resistance, most importantly the increasing recognition of isolates producing extended-spectrum β-lactamases (ESBL). Herein, we used whole-genome sequencing (WGS) on ExPEC isolates for a comprehensive genotypic characterization. Twenty-one ExPEC isolates, nine with and 12 without ESBL-production, from 16 patients with suspected sepsis were sequenced on an Illumina MiSeq platform. Analysis of WGS data was performed with widely used bioinformatics software and tools for genotypic characterization of the isolates. A higher number of plasmids, virulence and resistance genes were observed in the ESBL-producing isolates than the non-ESBL-producing, although not statistically significant due to the low sample size. All nine ESBL-producing ExPEC isolates presented with at least one bla gene, as did three of the 12 without ESBL-production. Multi-locus sequence typing analysis revealed a diversity of sequence types whereas phylogroup A prevailed among isolates both with and without ESBL-production. In conclusion, this limited study shows that analysis of WGS data can be used for genotypic characterization of ExPEC isolates to obtain in-depth information of clinical relevance.

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  • 37.
    Tilevik, Diana
    et al.
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Saxenborn, Patricia
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Tilevik, Andreas
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Fagerlind, Magnus
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Lubovac-Pilav, Zelmina
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    Enroth, Helena
    Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.
    Using next-generation sequencing to study biodiversity in Klebsiella spp. isolated from patients with suspected sepsis2019Conference paper (Refereed)
  • 38.
    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
    University of Skövde, School of Bioscience. University of Skövde, Systems Biology Research Environment.
    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 inhibitors2020In: Environmental Science and Pollution Research, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 27, no 22, p. 27279-27292Article in journal (Refereed)
    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. 

  • 39.
    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
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Nahar, Noor
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    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
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    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 Practices2017In: Handbook of Metal–Microbe Interactions and Bioremediation / [ed] Surajit Das, Hirak Ranjan Dash, Boca Raton, FL: CRC Press, 2017, p. 25-40Chapter in book (Refereed)
    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.

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