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Egorova, D., Olsson, B., Kir'yanova, T. & Plotnikova, E. (2024). An Assessment of the Degradation Potential and Genomic Insights Towards Hydroxylated Biphenyls by Rhodococcus opacus Strain KT112-7. Current Genomics
Open this publication in new window or tab >>An Assessment of the Degradation Potential and Genomic Insights Towards Hydroxylated Biphenyls by Rhodococcus opacus Strain KT112-7
2024 (English)In: Current Genomics, ISSN 1389-2029, E-ISSN 1875-5488Article in journal (Refereed) Epub ahead of print
Abstract [en]

Background: Hydroxylated biphenyls are currently recognized as secondary pollutants that are hazardous to animals and humans. Bacterial degradation is the most effective method for the degradation of hydroxylated biphenyls. Several strains capable of degrading polychlorinated biphenyls have been described, which also degrade hydroxylated biphenyls.

Objectives: 1) To study the biodegradative properties of the Rhodococcus opacus strain KT112-7 towards mono-hydroxylated biphenyls. 2) To analyze the genome of the Rhodococcus opacus strain KT112-7. 3) To identify the genetic basis for the unique biodegradative potential of the Rhodococcus opacus strain KT112-7.

Methods: A genome analysis of the strain KT112-7 was conducted based on whole-genome sequencing using various programs and databases (Velvet, CONTIGuator, RAST, KEGG) for annotation and identification of protein-coding sequences. The strain KT112-7 was cultivated in a K1 mineral medium supplemented with mono-hydroxy biphenyls or mono-hydroxybenzoic acids as the carbon source. For the growth test mono-hydroxybiphenyls or mono-hydroxybenzoic acids were dosed at concentrations of 0.5 g/L and 1.0 g/L correspondently, and the bacterial growth was monitored by the optical density. For the biodegradative activity test, mono-hydroxybiphenyls were dosed at a concentration of 0.1 g/L in vials, inoculated with late exponential phase bacteria previously acclimated on biphenyl. Compound analysis was performed using GC-MS, HPLC, and spectrophotometry.

Results: It was found that the genome of strain KT112-7 consists of a chromosome and 2 plasmids. Biphenyl degradation genes (bph genes) were identified on plasmid PRHWK1 and the chromosome, as well as hydroxybenzoic acid degradation genes on the chromosome. The strain KT112-7 was shown to degrade mono-hydroxylated biphenyls to basal metabolic compounds of the cell, with the highest destructive activity observed towards 3- and 4-hydroxylated biphenyls (98%).

Conclusion: The Rhodococcus opacus strain KT112-7 is characterized by genetic systems that contribute to its high biodegradative potential towards mono-hydroxylated biphenyls and their metabolites. Thus, the strain KT112-7 is promising for use in hydroxybiphenyl degradation technologies.

Place, publisher, year, edition, pages
Bentham Science Publishers, 2024
Keywords
Rhodococcus opacus, hydroxylated biphenyls, bph genes, degradation
National Category
Biochemistry and Molecular Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-24447 (URN)10.2174/0113892029319746240812051356 (DOI)001298872100001 ()2-s2.0-85208622725 (Scopus ID)
Note

Available online 21 August, 2024

Available from: 2024-08-23 Created: 2024-08-23 Last updated: 2024-11-21Bibliographically approved
Ekelund Ugge, G. M., Jonsson, A., Olsson, B., Sjöback, R. & Berglund, O. (2020). Transcriptional and biochemical biomarker responses in a freshwater mussel (Anodonta anatina) under environmentally relevant Cu exposure. Environmental Science and Pollution Research, 27(9), 9999-10010
Open this publication in new window or tab >>Transcriptional and biochemical biomarker responses in a freshwater mussel (Anodonta anatina) under environmentally relevant Cu exposure
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2020 (English)In: Environmental Science and Pollution Research, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 27, no 9, p. 9999-10010Article in journal (Refereed) Published
Abstract [en]

Molecular biomarkers, like gene transcripts or enzyme activities, are potentially powerful tools for early warning assessment of pollution. However, a thorough understanding of response and baseline variation is required to distinguish actual effects from pollution. Here, we assess the freshwater mussel Anodonta anatina as a biomarker model species for freshwater ecosystems, by testing responses of six transcriptional (cat, gst, hsp70, hsp90, mt, and sod) and two biochemical (AChE and GST) biomarkers to environmentally relevant Cu water concentrations. Mussels (n = 20), collected from a stream free from point source pollution, were exposed in the laboratory, for 96 h, to Cu treatments (< 0.2 mu g/L, 0.77 +/- 0.87 mu g/L, and 6.3 +/- 5.4 mu g/L). Gills and digestive glands were extracted and analyzed for transcriptional and biochemical responses. Biological and statistical effect sizes from Cu treatments were in general small (mean log(2) fold-change <= 0.80 and Cohen's f <= 0.69, respectively), and no significant treatment effects were observed. In contrast, four out of eight biomarkers (cat, gst, hsp70, and GST) showed a significant sex:tissue interaction, and additionally one (sod) showed significant overall effects from sex. Specifically, three markers in gills (cat, mt, GST) and one in digestive gland (AChE) displayed significant sex differences, independent of treatment. Results suggest that sex or tissue effects might obscure low-magnitude biomarker responses and potential early warnings. Thus, variation in biomarker baselines and response patterns needs to be further addressed for the future use of A. anatina as a biomarker model species.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2020
Keywords
Bivalve, Gene expression, Response variability, Sex effects, Effect size, RT-qPCR
National Category
Other Biological Topics
Research subject
INF502 Biomarkers; Ecological Modelling Group; Bioinformatics
Identifiers
urn:nbn:se:his:diva-18132 (URN)10.1007/s11356-020-07660-4 (DOI)000524949600099 ()31933076 (PubMedID)2-s2.0-85077999744 (Scopus ID)
Funder
Knowledge Foundation
Note

CC BY 4.0

Environmental Science and Pollution Research. ISSN: 0944-1344 (Print) 1614-7499 (Online)

Available from: 2020-01-14 Created: 2020-01-14 Last updated: 2023-01-12Bibliographically approved
Weishaupt, H., Johansson, P., Sundström, A., Lubovac-Pilav, Z., Olsson, B., Nelander, S. & Swartling, F. J. (2019). Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes. Bioinformatics, 35(18), 3357-3364
Open this publication in new window or tab >>Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes
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2019 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, no 18, p. 3357-3364Article in journal (Refereed) Published
Abstract [en]

Motivation: Medulloblastoma (MB) is a brain cancer predominantly arising in children. Roughly 70% of patients are cured today, but survivors often suffer from severe sequelae. MB has been extensively studied by molecular profiling, but often in small and scattered cohorts. To improve cure rates and reduce treatment side effects, accurate integration of such data to increase analytical power will be important, if not essential.

Results: We have integrated 23 transcription datasets, spanning 1350 MB and 291 normal brain samples. To remove batch effects, we combined the Removal of Unwanted Variation (RUV) method with a novel pipeline for determining empirical negative control genes and a panel of metrics to evaluate normalization performance. The documented approach enabled the removal of a majority of batch effects, producing a large-scale, integrative dataset of MB and cerebellar expression data. The proposed strategy will be broadly applicable for accurate integration of data and incorporation of normal reference samples for studies of various diseases. We hope that the integrated dataset will improve current research in the field of MB by allowing more large-scale gene expression analyses.

Place, publisher, year, edition, pages
Oxford University Press, 2019
National Category
Bioinformatics and Computational Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-16769 (URN)10.1093/bioinformatics/btz066 (DOI)000487327500019 ()30715209 (PubMedID)2-s2.0-85072349088 (Scopus ID)
Note

CC BY-NC 4.0

Available from: 2019-04-11 Created: 2019-04-11 Last updated: 2025-02-07Bibliographically approved
Sedghi, M., Salari, M., Moslemi, A.-R., Kariminejad, A., Davis, M., Goullée, H., . . . Tajsharghi, H. (2018). Ataxia-telangiectasia-like disorder in a family deficient for MRE11A, caused by a MRE11 variant. Neurology: Genetics, 4(6), Article ID e295.
Open this publication in new window or tab >>Ataxia-telangiectasia-like disorder in a family deficient for MRE11A, caused by a MRE11 variant
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2018 (English)In: Neurology: Genetics, ISSN 2376-7839, Vol. 4, no 6, article id e295Article in journal (Refereed) Published
Abstract [en]

Objective We report 3 siblings with the characteristic features of ataxia-telangiectasia-like disorder associated with a homozygous MRE11 synonymous variant causing nonsense-mediated mRNA decay (NMD) and MRE11A deficiency. Methods Clinical assessments, next-generation sequencing, transcript and immunohistochemistry analyses were performed. Results The patients presented with poor balance, developmental delay during the first year of age, and suffered from intellectual disability from early childhood. They showed oculomotor apraxia, slurred and explosive speech, limb and gait ataxia, exaggerated deep tendon reflex, dystonic posture, and mirror movement in their hands. They developed mild cognitive abilities. Brain MRI in the index case revealed cerebellar atrophy. Next-generation sequencing revealed a homozygous synonymous variant in MRE11 (c.657C>T, p.Asn219=) that we show affects splicing. A complete absence of MRE11 transcripts in the index case suggested NMD and immunohistochemistry confirmed the absence of a stable protein. Conclusions Despite the critical role of MRE11A in double-strand break repair and its contribution to the Mre11/Rad50/Nbs1 complex, the absence of MRE11A is compatible with life. 

Place, publisher, year, edition, pages
Lippincott Williams & Wilkins, 2018
National Category
Clinical Laboratory Medicine
Research subject
Bioinformatics; Translational Medicine TRIM
Identifiers
urn:nbn:se:his:diva-16631 (URN)10.1212/NXG.0000000000000295 (DOI)000455099800019 ()30584599 (PubMedID)2-s2.0-85060870481 (Scopus ID)
Note

CC BY 4.0

From the Medical Genetics Laboratory (M. Sedghi), Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Neurology (M. Salari), Shahid Beheshti University of Medical Science, Tehran, Iran; Department of Pathology (A.-R.M.), University of Gothenburg, Sahlgrenska University Hospital, Sweden; Kariminejad-Najmabadi Pathology & Genetics Center (A.K.), Tehran, Iran; Department of Diagnostic Genomics (M.D.), Pathwest, QEII Medical Centre; Centre for Medical Research (H.G., N.L., H.T.), The University of Western Australia and the Harry Perkins Institute for Medical Research, Nedlands, Australia; School of Bioscience (B.O.), University of Skovde; and Division Biomedicine (H.T.), School of Health and Education, University of Skovde, Sweden.

Available from: 2019-02-15 Created: 2019-02-15 Last updated: 2023-09-21
Olsson, B. E., Korsakova, E. S., Anan'ina, L. N., Pyankova, A. A., Mavrodi, O. V., Plotnikova, E. G. & Mavrodi, D. V. (2017). Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia. Standards in Genomic Sciences, 12(39), 1-13
Open this publication in new window or tab >>Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia
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2017 (English)In: Standards in Genomic Sciences, E-ISSN 1944-3277, Vol. 12, no 39, p. 1-13Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
BioMed Central, 2017
Keywords
Chromohalobacter, Halomonadaceae, Halophile, Potash mine tailings, Salinicola
National Category
Bioinformatics and Computational Biology Microbiology Genetics and Genomics
Research subject
Bioinformatics; INF501 Integration of -omics Data
Identifiers
urn:nbn:se:his:diva-13940 (URN)10.1186/s40793-017-0251-5 (DOI)000406197200001 ()28729898 (PubMedID)2-s2.0-85027150301 (Scopus ID)
Note

CC BY 4.0

Available from: 2017-07-23 Created: 2017-07-23 Last updated: 2025-02-05Bibliographically approved
Rahman, A., Olsson, B., Jass, J., Nawani, N., Ghosh, S. & Mandal, A. (2017). Genome Sequencing Revealed Chromium and Other Heavy Metal Resistance Genes in E. cloacae B2-Dha. Journal of Microbial & Biochemical Technology, 9(5), 191-199
Open this publication in new window or tab >>Genome Sequencing Revealed Chromium and Other Heavy Metal Resistance Genes in E. cloacae B2-Dha
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2017 (English)In: Journal of Microbial & Biochemical Technology, E-ISSN 1948-5948, Vol. 9, no 5, p. 191-199Article in journal (Refereed) Published
Abstract [en]

The previously described chromium resistant bacterium, Enterobacter cloacae B2-DHA, was isolated from leather manufacturing tannery landfill in Bangladesh. Here we report the entire genome sequence of this bacterium containing chromium and other heavy metal resistance genes. The genome size and the number of genes, determined by massive parallel sequencing and comparative analysis with other known Enterobacter genomes, are predicted to be 4.22 Mb and 3958, respectively. Nearly 160 of these genes were found to be involved in binding, transport, and catabolism of ions as well as efflux of inorganic and organic compounds. Specifically, the presence of two chromium resistance genes, chrR and chrA was verified by polymerase chain reaction. The outcome of this research highlights the significance of this bacterium in bioremediation of chromium and other toxic metals from the contaminated sources.

Place, publisher, year, edition, pages
Omics Publishing Group, 2017
Keywords
Genome Sequencing, Bioremediation, Toxic metals, Enterobacter cloacae, Gene annotation
National Category
Bioinformatics and Computational Biology
Research subject
Biotechnology; Bioinformatics; INF501 Integration of -omics Data
Identifiers
urn:nbn:se:his:diva-14401 (URN)10.4172/1948-5948.1000365 (DOI)
Note

CC BY

Available from: 2017-11-14 Created: 2017-11-14 Last updated: 2025-02-07Bibliographically approved
Rahman, A., Nahar, N., Olsson, B. & Mandal, A. (2016). Complete Genome Sequence of Enterobacter cloacae B2-DHA: a Chromium-Resistant Bacterium. Genome Announcements, 4(3), Article ID e00483-16.
Open this publication in new window or tab >>Complete Genome Sequence of Enterobacter cloacae B2-DHA: a Chromium-Resistant Bacterium
2016 (English)In: Genome Announcements, E-ISSN 2169-8287, Vol. 4, no 3, article id e00483-16Article in journal (Refereed) Published
Abstract [en]

Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size.

Place, publisher, year, edition, pages
American Society for Microbiology, 2016
Keywords
Enterobacter cloacae, Genome sequencing, de novo assembly, Gene annotation
National Category
Bioinformatics and Computational Biology
Research subject
Bioinformatics; Biotechnology
Identifiers
urn:nbn:se:his:diva-12317 (URN)10.1128/genomeA.00483-16 (DOI)000460660100145 ()27257201 (PubMedID)2-s2.0-85009965114 (Scopus ID)
Note

CC BY 4.0

Available from: 2016-06-01 Created: 2016-06-01 Last updated: 2025-02-07Bibliographically approved
Rahman, A., Nahar, N., Jass, J., Olsson, B. & Mandal, A. (2016). Complete genome sequence of Lysinibacillus sphaericus B1-CDA: a bacterium that accumulates arsenics. Genome Announcements, 4(1), Article ID e00999-15.
Open this publication in new window or tab >>Complete genome sequence of Lysinibacillus sphaericus B1-CDA: a bacterium that accumulates arsenics
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2016 (English)In: Genome Announcements, E-ISSN 2169-8287, Vol. 4, no 1, article id e00999-15Article in journal (Refereed) Published
Abstract [en]

Here, we report the genomic sequence and genetic composition of an arsenic resistant bacterium Lysinibacillus sphaericus B1-CDA. Assembly of the sequencing reads revealed that the genome size is ~4.5 Mb encompassing ~80% of the chromosomal DNA.

Place, publisher, year, edition, pages
American Society for Microbiology, 2016
National Category
Bioinformatics and Computational Biology
Research subject
Natural sciences; Bioinformatics
Identifiers
urn:nbn:se:his:diva-11733 (URN)10.1128/genomeA.00999-15 (DOI)000460649500018 ()26798084 (PubMedID)2-s2.0-85009977094 (Scopus ID)
Note

CC BY 3.0

Available from: 2015-12-01 Created: 2015-12-01 Last updated: 2025-02-07Bibliographically approved
Ghosheh, N., Olsson, B., Edsbagge, J., Küppers-Munther, B., Van Giezen, M., Asplund, A., . . . Synnergren, J. (2016). Highly Synchronized Expression of Lineage-Specific Genes during In Vitro Hepatic Differentiation of Human Pluripotent Stem Cell Lines. Stem Cells International, 2016, Article ID 8648356.
Open this publication in new window or tab >>Highly Synchronized Expression of Lineage-Specific Genes during In Vitro Hepatic Differentiation of Human Pluripotent Stem Cell Lines
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2016 (English)In: Stem Cells International, ISSN 1687-9678, Vol. 2016, article id 8648356Article in journal (Refereed) Published
Abstract [en]

Human pluripotent stem cells- (hPSCs-) derived hepatocytes have the potential to replace many hepatic models in drug discovery and provide a cell source for regenerative medicine applications. However, the generation of fully functional hPSC-derived hepatocytes is still a challenge. Towards gaining better understanding of the differentiation and maturation process, we employed a standardized protocol to differentiate six hPSC lines into hepatocytes and investigated the synchronicity of the hPSC lines by applying RT-qPCR to assess the expression of lineage-specific genes (OCT4, NANOG, T, SOX17, CXCR4, CER1, HHEX, TBX3, PROX1, HNF6, AFP, HNF4a, KRT18, ALB, AAT, and CYP3A4) which serve as markers for different stages during liver development. The data was evaluated using correlation and clustering analysis, demonstrating that the expression of these markers is highly synchronized and correlated well across all cell lines. The analysis also revealed a distribution of the markers in groups reflecting the developmental stages of hepatocytes. Functional analysis of the differentiated cells further confirmed their hepatic phenotype. Taken together, these results demonstrate, on the molecular level, the highly synchronized differentiation pattern across multiple hPSC lines. Moreover, this study provides additional understanding for future efforts to improve the functionality of hPSC-derived hepatocytes and thereby increase the value of related models.

Place, publisher, year, edition, pages
Hindawi Publishing Corporation, 2016
National Category
Cell Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-12033 (URN)10.1155/2016/8648356 (DOI)000373503900001 ()26949401 (PubMedID)2-s2.0-84959330405 (Scopus ID)
Funder
Knowledge Foundation, 012/0310Knowledge Foundation, 2013/89
Note

CC BY 4.0

Correspondence should be addressed to Nidal Ghosheh; nidal.ghosheh@his.se

Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2023-01-04Bibliographically approved
Visuttijai, K., Pettersson, J., Mehrbani Azar, Y., van den Bout, I., Örndal, C., Marcickiewicz, J., . . . Behboudi, A. (2016). Lowered Expression of Tumor Suppressor Candidate MYO1C Stimulates Cell Proliferation, Suppresses Cell Adhesion and Activates AKT. PLOS ONE, 11(10), Article ID e0164063.
Open this publication in new window or tab >>Lowered Expression of Tumor Suppressor Candidate MYO1C Stimulates Cell Proliferation, Suppresses Cell Adhesion and Activates AKT
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2016 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 10, article id e0164063Article in journal (Refereed) Published
Abstract [en]

Myosin-1C (MYO1C) is a tumor suppressor candidate located in a region of recurrent losses distal to TP53. Myo1c can tightly and specifically bind to PIP2, the substrate of Phosphoinositide 3-kinase (PI3K), and to Rictor, suggesting a role for MYO1C in the PI3K pathway. This study was designed to examine MYO1C expression status in a panel of well-stratified endometrial carcinomas as well as to assess the biological significance of MYO1C as a tumor suppressor in vitro. We found a significant correlation between the tumor stage and lowered expression of MYO1C in endometrial carcinoma samples. In cell transfection experiments, we found a negative correlation between MYO1C expression and cell proliferation, and MYO1C silencing resulted in diminished cell migration and adhesion. Cells expressing excess of MYO1C had low basal level of phosphorylated protein kinase B (PKB, a.k.a. AKT) and cells with knocked down MYO1C expression showed a quicker phosphorylated AKT (pAKT) response in reaction to serum stimulation. Taken together the present study gives further evidence for tumor suppressor activity of MYO1C and suggests MYO1C mediates its tumor suppressor function through inhibition of PI3K pathway and its involvement in loss of contact inhibition.

Place, publisher, year, edition, pages
Public Library of Science, 2016
Keywords
MYO1C, myosin-1c, tumor suppressor, AKT signaling
National Category
Other Medical Sciences
Research subject
Medical sciences; Bioinformatics
Identifiers
urn:nbn:se:his:diva-13020 (URN)10.1371/journal.pone.0164063 (DOI)000385698100017 ()27716847 (PubMedID)2-s2.0-84991449467 (Scopus ID)
Projects
Cellular, Molecular and Functional Characterization of the Tumor Suppressor Candidate MYO1C
Note

CC BY 4.0

Available from: 2016-10-11 Created: 2016-10-11 Last updated: 2023-09-21
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6254-4335

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