his.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 88) Show all publications
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
Show others...
2017 (English)In: Standards in Genomic Sciences, ISSN 1944-3277, 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.

Keywords
Chromohalobacter, Halomonadaceae, Halophile, Potash mine tailings, Salinicola
National Category
Bioinformatics and Systems Biology Microbiology Genetics
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-13940 (URN)10.1186/s40793-017-0251-5 (DOI)000406197200001 ()28729898 (PubMedID)2-s2.0-85027150301 (Scopus ID)
Available from: 2017-07-23 Created: 2017-07-23 Last updated: 2017-11-29Bibliographically 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
Show others...
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 Systems Biology
Research subject
Biotechnology; Bioinformatics
Identifiers
urn:nbn:se:his:diva-14401 (URN)10.4172/1948-5948.1000365 (DOI)
Available from: 2017-11-14 Created: 2017-11-14 Last updated: 2018-06-27Bibliographically 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, ISSN 2169-8287, 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 Systems Biology
Research subject
Bioinformatics; Biotechnology
Identifiers
urn:nbn:se:his:diva-12317 (URN)10.1128/genomeA.00483-16 (DOI)27257201 (PubMedID)2-s2.0-85009965114 (Scopus ID)
Available from: 2016-06-01 Created: 2016-06-01 Last updated: 2018-08-23Bibliographically 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
Show others...
2016 (English)In: Genome Announcements, ISSN 2169-8287, 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 Microbiolology, 2016
National Category
Bioinformatics and Systems Biology
Research subject
Natural sciences; Bioinformatics
Identifiers
urn:nbn:se:his:diva-11733 (URN)10.1128/genomeA.00999-15 (DOI)26798084 (PubMedID)2-s2.0-85009977094 (Scopus ID)
Available from: 2015-12-01 Created: 2015-12-01 Last updated: 2018-08-23Bibliographically 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
Show others...
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.

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)
Available from: 2016-03-14 Created: 2016-03-14 Last updated: 2018-07-31Bibliographically 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 MYO1CStimulates 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 MYO1CStimulates Cell Proliferation, Suppresses Cell Adhesion and Activates AKT
Show others...
2016 (English)In: PLoS ONE, ISSN 1932-6203, 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.

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
Available from: 2016-10-11 Created: 2016-10-11 Last updated: 2018-07-31
Kariminejad, A., Almadani, N., Khoshaeen, A., Olsson, B., Moslemi, A.-R. & Tajsharghi, H. (2016). Truncating CHRNG mutations associated with interfamilial variability of the severity of the Escobar variant of multiple pterygium syndrome. BMC Genetics, 17(1), Article ID 71.
Open this publication in new window or tab >>Truncating CHRNG mutations associated with interfamilial variability of the severity of the Escobar variant of multiple pterygium syndrome
Show others...
2016 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 17, no 1, article id 71Article in journal (Refereed) Published
Abstract [en]

BACKGROUND:In humans, muscle-specific nicotinergic acetylcholine receptor (AChR) is a transmembrane protein with five different subunits, coded by CHRNA1, CHRNB, CHRND and CHRNG/CHRNE. The gamma subunit of AChR encoded by CHRNG is expressed during early foetal development, whereas in the adult, the γ subunit is replaced by a ε subunit. Mutations in the CHRNG encoding the embryonal acetylcholine receptor may cause the non-lethal Escobar variant (EVMPS) and lethal form (LMPS) of multiple pterygium syndrome. The MPS is a condition characterised by prenatal growth failure with pterygium and akinesia leading to muscle weakness and severe congenital contractures, as well as scoliosis.

RESULTS:Our whole exome sequencing studies have identified one novel and two previously reported homozygous mutations in CHRNG in three families affected by non-lethal EVMPS. The mutations consist of deletion of two nucleotides, cause a frameshift predicted to result in premature termination of the foetally expressed gamma subunit of the AChR.

CONCLUSIONS:Our data suggest that severity of the phenotype varies significantly both within and between families with MPS and that there is no apparent correlation between mutation position and clinical phenotype. Although individuals with CHRNG mutations can survive, there is an increased frequency of abortions and stillbirth in their families. Furthermore, genetic background and environmental modifiers might be of significance for decisiveness of the lethal spectrum, rather than the state of the mutation per se. Detailed clinical examination of our patients further indicates the changing phenotype from infancy to childhood.

Place, publisher, year, edition, pages
BioMed Central, 2016
Keywords
severe genetic disorder
National Category
Clinical Medicine
Research subject
Medical sciences; Bioinformatics; Biomedical Genetics
Identifiers
urn:nbn:se:his:diva-12337 (URN)10.1186/s12863-016-0382-5 (DOI)000377077500001 ()27245440 (PubMedID)2-s2.0-84971537060 (Scopus ID)
Funder
Swedish Research Council
Available from: 2016-06-08 Created: 2016-06-08 Last updated: 2018-07-31Bibliographically approved
Jurcevic, S., Klinga-Levan, K., Olsson, B. & Ejeskär, K. (2016). Verification of microRNA expression in human endometrial adenocarcinoma. BMC Cancer, 16(1), Article ID 261.
Open this publication in new window or tab >>Verification of microRNA expression in human endometrial adenocarcinoma
2016 (English)In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 16, no 1, article id 261Article in journal (Refereed) Published
Place, publisher, year, edition, pages
BioMed Central, 2016
National Category
Cancer and Oncology
Research subject
Biomedical Genetics; Bioinformatics
Identifiers
urn:nbn:se:his:diva-10890 (URN)10.1186/s12885-016-2296-z (DOI)000373329900001 ()27039384 (PubMedID)2-s2.0-84962003924 (Scopus ID)
Available from: 2015-05-05 Created: 2015-05-05 Last updated: 2018-07-31Bibliographically approved
Rahman, A., Nahar, N., Nawani, N. N., Jass, J., Hossain, K., Alam Saud, Z., . . . Mandal, A. (2015). Bioremediation of hexavalent chromium (VI) by a soil borne bacterium, Enterobacter cloacae B2-DHA. Journal of Environmental Science and Health. Part A: Toxic/Hazardous Substances and Environmental Engineering, 50(11), 1136-1147
Open this publication in new window or tab >>Bioremediation of hexavalent chromium (VI) by a soil borne bacterium, Enterobacter cloacae B2-DHA
Show others...
2015 (English)In: 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) Published
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.

Place, publisher, year, edition, pages
Taylor & Francis, 2015
Keywords
Bioremediation, Chromium, Enterobacter cloacae, Human Health, Tannery Effluents, Soil Borne Bacterium
National Category
Microbiology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-10916 (URN)10.1080/10934529.2015.1047670 (DOI)000359339900006 ()26191988 (PubMedID)2-s2.0-84937800926 (Scopus ID)
Available from: 2015-05-11 Created: 2015-05-11 Last updated: 2018-07-31Bibliographically approved
Rahman, A., Nahar, N., Nawani, N. N., Jass, J., Ghosh, S., Olsson, B. & Mandal, A. (2015). Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Genomics, 106(6), 384-392
Open this publication in new window or tab >>Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics
Show others...
2015 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 106, no 6, p. 384-392Article in journal (Refereed) Published
Abstract [en]

Previously, we reported an arsenic resistant bacterium Lysinibacillus sphaericus B1-CDA, isolated from an arsenic contaminated lands. Here, we have investigated its genetic composition and evolutionary history by using massively parallel sequencing and comparative analysis with other known Lysinibacillus genomes. Assembly of the sequencing reads revealed a genome of ~ 4.5 Mb in size encompassing ~ 80% of the chromosomal DNA. We found that the set of ordered contigs contains abundant regions of similarity with other Lysinibacillus genomes and clearly identifiable genome rearrangements. Furthermore, all genes of B1-CDA that were predicted be involved in its resistance to arsenic and/or other heavy metals were annotated. The presence of arsenic responsive genes was verified by PCR in vitro conditions. The findings of this study highlight the significance of this bacterium in removing arsenics and other toxic metals from the contaminated sources. The genetic mechanisms of the isolate could be used to cope with arsenic toxicity.

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
Toxic metals, Bioremediation, Genome sequencing, de novo assembly
National Category
Biochemistry and Molecular Biology Bioinformatics and Systems Biology
Research subject
Natural sciences; Bioinformatics; Biotechnology
Identifiers
urn:nbn:se:his:diva-11575 (URN)10.1016/j.ygeno.2015.09.006 (DOI)000365613100010 ()26387925 (PubMedID)2-s2.0-84948102629 (Scopus ID)
Projects
Bioremediation
Funder
Sida - Swedish International Development Cooperation Agency, AKT-2010-18
Available from: 2015-10-02 Created: 2015-10-01 Last updated: 2018-07-31Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6254-4335

Search in DiVA

Show all publications