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Allochthonous inputs of riverine picocyanobacteria to coastal waters in the Arctic Ocean.

https://arctichealth.org/en/permalink/ahliterature95689
Source
FEMS Microbiol Ecol. 2007 Feb;59(2):356-65
Publication Type
Article
Date
Feb-2007
Author
Waleron Malgorzata
Waleron Krzysztof
Vincent Warwick F
Wilmotte Annick
Author Affiliation
Centre for Protein Engineering, Institute of Chemistry B6, Sart Tilman, University of Liège, Liège, Belgium.
Source
FEMS Microbiol Ecol. 2007 Feb;59(2):356-65
Date
Feb-2007
Language
English
Publication Type
Article
Keywords
Arctic Regions
Climate
Cyanobacteria - classification - genetics
DNA, Bacterial - analysis
DNA, Ribosomal - analysis
Gene Library
Molecular Sequence Data
Phylogeny
Plastids - genetics
RNA, Ribosomal, 16S - genetics
Rivers - microbiology
Seawater - microbiology
Sequence Analysis, DNA
Abstract
The observed onset of climate change at high northern latitudes has highlighted the need to establish current baseline conditions in the Arctic Ocean, and has raised concern about the potential for the invasion and growth of biota that have warm temperature optima, such as cyanobacteria. In this study, we used 16S rRNA gene sequences as a molecular marker to evaluate the hypothesis that Arctic rivers provide a major inoculum of cyanobacteria into the coastal Arctic Ocean. Surface samples were collected along a transect extending from the Mackenzie River (Northwest Territories, Canada), across its estuary, to 200 km offshore at the edge of the perennial Arctic pack ice (Beaufort Sea). The highest picocyanobacteria concentrations occurred in the river, with concentrations an order of magnitude lower at offshore marine stations. The 16S rRNA gene clone libraries of five surface samples and five strains along this gradient showed that the cyanobacterial sequences were divided into eight operational taxonomic units (OTUs), six OTUs closely related to freshwater and brackish Synechococcus and two OTUs of filamentous cyanobacteria. No typically marine Synechococcus sequences and no Prochlorococcus sequences were recovered. These results are consistent with the hypothesis of an allochthonous origin of picocyanobacteria in the coastal Arctic Ocean, and imply survival but little net growth of picocyanobacteria under the present conditions in northern high-latitude seas.
PubMed ID
17132157 View in PubMed
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An exploratory study of microbial diversity in sinus infections of cystic fibrosis patients by molecular methods.

https://arctichealth.org/en/permalink/ahliterature266112
Source
J Cyst Fibros. 2014 Dec;13(6):645-52
Publication Type
Article
Date
Dec-2014
Author
Vibeke Børsholt Rudkjøbing
Kasper Aanaes
Tine Yding Wolff
Christian von Buchwald
Helle Krogh Johansen
Trine Rolighed Thomsen
Source
J Cyst Fibros. 2014 Dec;13(6):645-52
Date
Dec-2014
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Bacteria, Aerobic - isolation & purification
Bacteria, Anaerobic - isolation & purification
Bacterial Infections - diagnosis - microbiology - therapy
Child
Cystic Fibrosis - complications - microbiology
DNA, Bacterial - isolation & purification
Denmark
Endoscopy
Female
Gene Library
Humans
Male
Middle Aged
Polymerase Chain Reaction
RNA, Ribosomal, 16S
Sinusitis - microbiology - surgery
Young Adult
Abstract
For the first time microorganisms in CF sinuses are investigated by molecular methods in response to an absence of anaerobes in CF sinus samples during a two-year period at the Copenhagen CF center.
Endoscopic sinus surgery was performed in 19 CF patients. DNA from intact bacterial cells was investigated by 16S rRNA gene analysis and quantitative PCR. Results were compared to culture-dependent routine diagnosis.
Molecular methods showed a large microbial diversity, which included undetected anaerobes that may play a pathogenic role. Importantly, the culture methods did not always detect known CF pathogens. Quantitative PCR showed generally a higher abundance of classic CF pathogens e.g. Pseudomonas aeruginosa and Staphylococcus aureus compared with the anaerobe Propionibacterium acnes.
The results indicate that the culture methods in some cases may not be suitable as stand-alone method for this patient group, as diversity may be underestimated and important species undetected.
PubMed ID
24636809 View in PubMed
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Assembly of a 1-Mb restriction-mapped cosmid contig spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1.

https://arctichealth.org/en/permalink/ahliterature211815
Source
Genomics. 1996 Jun 1;34(2):223-5
Publication Type
Article
Date
Jun-1-1996
Author
A S Olsen
A. Georgescu
S. Johnson
A V Carrano
Author Affiliation
Human Genome Center, Lawrence Livermore National Laboratory, Livermore, California, 94551, USA.
Source
Genomics. 1996 Jun 1;34(2):223-5
Date
Jun-1-1996
Language
English
Publication Type
Article
Keywords
Chromosome Mapping
Chromosomes, Human, Pair 19
Cloning, Molecular
Cosmids
Deoxyribonuclease EcoRI
Exons
Finland - epidemiology
Gene Library
Genes, Recessive
Genetic markers
Humans
Incidence
Nephrosis - congenital - epidemiology - genetics
Restriction Mapping
Abstract
We describe the assembly of a 1-Mb cosmid contig and restriction map spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1. The map was constructed from 16 smaller contigs assembled by fingerprinting, a BAC and a PAC clone, and 42 previously unmapped cosmids. In most cases, single-step cosmid walks were sufficient to join two previously assembled contigs, and all but one gap was filled from this cosmid contig library. The remaining gap of about 19 kb was spanned with a single BAC and a single PAC clone. EcoRI mapping of a dense set of overlapping clones validated the assembly of the map and indicated a length of 1040 kb for the contig. This high-resolution clone map provides an ideal resource for gene identification through cDNA selection, exon trapping, and DNA sequencing.
PubMed ID
8661053 View in PubMed
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Association of an X-chromosome dodecamer insertional variant allele with mental retardation.

https://arctichealth.org/en/permalink/ahliterature204843
Source
Mol Psychiatry. 1998 Jul;3(4):303-9
Publication Type
Article
Date
Jul-1998
Author
R A Philibert
B H King
S. Winfield
E H Cook
Y H Lee
B. Stubblefield
P. Damschroder-Williams
C. Dea
A. Palotie
C. Tengstrom
B M Martin
E I Ginns
Author Affiliation
Clinical Neuroscience Branch, National Institute of Mental Health, Bethesda, MD 20892, USA. philiber@irp.nimh.nih.gov
Source
Mol Psychiatry. 1998 Jul;3(4):303-9
Date
Jul-1998
Language
English
Publication Type
Article
Keywords
Alleles
Amino Acid Sequence
Animals
Base Sequence
California - epidemiology
Chromosome Mapping
Conserved Sequence
Cosmids
DNA Transposable Elements
Europe - epidemiology
Exons
Female
Finland - epidemiology
Fragile X Syndrome - genetics
Gene Library
Genetic Variation
Humans
Hypothyroidism - epidemiology - genetics
In Situ Hybridization, Fluorescence
Intellectual Disability - genetics
Male
Mice
Molecular Sequence Data
Polymorphism, Genetic
Prevalence
Sequence Alignment
Sequence Homology, Amino Acid
Trinucleotide Repeats
X Chromosome
Abstract
Mental retardation is a prominent feature of many neurodevelopmental syndromes. In an attempt to identify genetic components of these illnesses, we isolated and sequenced a large number of human genomic cosmid inserts containing large trinucleotide repeats. One of these cosmids, Cos-4, maps to the X-chromosome and contains the sequence of a 7.3-kb mRNA. Initial polymorphism analysis across a region of repetitive DNA in this gene revealed a rare 12-bp exonic variation (
Notes
Erratum In: Mol Psychiatry 1999 Mar;4(2):197
PubMed ID
9702738 View in PubMed
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Autoantigens identified by screening a human heart cDNA library with acute rheumatic fever sera.

https://arctichealth.org/en/permalink/ahliterature148517
Source
Ann N Y Acad Sci. 2009 Sep;1173:83-91
Publication Type
Article
Date
Sep-2009
Author
Rebecca J Towers
Maike Bolm
Bart J Currie
Gursharan S Chhatwal
Peter K Fagan
Author Affiliation
Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Darwin, Australia. rebecca.towers@menzies.edu.au
Source
Ann N Y Acad Sci. 2009 Sep;1173:83-91
Date
Sep-2009
Language
English
Publication Type
Article
Keywords
Acute Disease
Adult
Autoantigens - immunology
Carrier Proteins - immunology - metabolism
DNA, Complementary - genetics - immunology
Enzyme-Linked Immunosorbent Assay - methods
Escherichia coli - genetics
Gene Library
Humans
Immunoglobulin Heavy Chains - immunology - metabolism
Mediator Complex
Microfilament Proteins - immunology - metabolism
Middle Aged
Myocardium - metabolism
Myosin Light Chains - immunology - metabolism
Nerve Tissue Proteins - immunology - metabolism
Nuclear Proteins - immunology - metabolism
Recombinant Proteins - immunology - metabolism
Rheumatic Fever - blood - diagnosis - immunology
Transcription Factors - immunology - metabolism
alpha Catenin - immunology - metabolism
Abstract
Acute rheumatic fever (ARF) is an autoimmune sequela of group A streptococcal infection mostly affecting school-aged children. Recurrent episodes of ARF can result in the development of rheumatic heart disease (RHD). One in 40 indigenous Australians in the Northern Territory is affected by RHD. This disease mostly impacts young people; 45% of those who require heart valve surgery in Australia due to RHD are younger than 25 years old. ARF is characterized by autoimmune attack of the heart; therefore, the presence of the autoantibodies involved could potentially be used to diagnose ARF. To this end, a human heart cDNA library was screened with serum from a patient with ARF, and 12 autoreactive human heart antigens were identified. They include five different IgG heavy chains and a range of tissue-specific cell-signaling proteins, species of which have been implicated in other autoimmune diseases. Preliminary ELISA results show that ARF patients have significantly higher levels of antibodies recognizing the cardiac autoantigens than controls. These antigens are promising candidates for the development of a serological assay for the diagnosis of ARF. The nature of the proteins identified has exciting implications for future research into the pathogenesis of ARF.
PubMed ID
19758136 View in PubMed
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Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern Siberia.

https://arctichealth.org/en/permalink/ahliterature95449
Source
Can J Microbiol. 2009 Jan;55(1):73-83
Publication Type
Article
Date
Jan-2009
Author
Wagner Dirk
Kobabe Svenja
Liebner Susanne
Author Affiliation
Alfred Wegener Institute for Polar and Marine Research, Research Unit Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany. Dirk.Wagner@awi.de
Source
Can J Microbiol. 2009 Jan;55(1):73-83
Date
Jan-2009
Language
English
Publication Type
Article
Keywords
Aerobiosis
Anaerobiosis
Bacteria - classification - genetics - isolation & purification - metabolism
Biodiversity
Carbon - metabolism
Cold Temperature
DNA, Bacterial - genetics
Gene Library
Genes, rRNA
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Siberia
Soil - analysis
Soil Microbiology
Abstract
Arctic permafrost environments store large amounts of organic carbon. As a result of global warming, intensified permafrost degradation and release of significant quantities of the currently conserved organic matter is predicted for high latitudes. To improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, the present study investigates structure and carbon turnover of the bacterial community in a permafrost-affected soil of the Lena Delta (72 degrees 22'N, 126 degrees 28'E) in northeastern Siberia. 16S rRNA gene clone libraries revealed the presence of all major soil bacterial groups and of the canditate divisions OD1 and OP11. A shift within the bacterial community was observed along the soil profile indicated by the absence of Alphaproteobacteria and Betaproteobacteria and a simultaneous increase in abundance and diversity of fermenting bacteria like Firmicutes and Actinobacteria near the permafrost table. BIOLOG EcoPlates were used to describe the spectrum of utilized carbon sources of the bacterial community in different horizons under in situ temperature conditions in the presence and absence of oxygen. The results revealed distinct qualitative differences in the substrates used and the turnover rates under oxic and anoxic conditions. It can be concluded that constantly negative redox potentials as characteristic for the near permafrost table horizons of the investigated soil did effectively shape the structure of the indigenous bacterial community limiting its phylum-level diversity and carbon turnover capacity.
PubMed ID
19190703 View in PubMed
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Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard.

https://arctichealth.org/en/permalink/ahliterature98372
Source
BMC Microbiol. 2010;10:10
Publication Type
Article
Date
2010
Author
Trine Glad
PÃ¥l Bernhardsen
Kaare M Nielsen
Lorenzo Brusetti
Magnus Andersen
Jon Aars
Monica A Sundset
Author Affiliation
Department of Pharmacy, University of Tromsø, 9037 Tromsø, Norway. trine.glad@uit.no.
Source
BMC Microbiol. 2010;10:10
Date
2010
Language
English
Publication Type
Article
Keywords
Animals
Bacteria - classification - genetics
Biodiversity
Feces - microbiology
Female
Gene Library
Male
Phylogeny
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
Sequence Analysis, RNA
Svalbard
Ursidae - microbiology
Abstract
BACKGROUND: Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81 degrees N, 10-33 degrees E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. RESULTS: A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 x 10(4) to 1.6 x 10(6) colony forming units (cfu)/ml for the rectum swabs and 4.0 x 10(3) to 1.0 x 10(5) cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic beta-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. CONCLUSION: The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.
PubMed ID
20074323 View in PubMed
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Building a DNA barcode library of Alaska's non-marine arthropods.

https://arctichealth.org/en/permalink/ahliterature281301
Source
Genome. 2017 Mar;60(3):248-259
Publication Type
Article
Date
Mar-2017
Author
Derek S Sikes
Matthew Bowser
John M Morton
Casey Bickford
Sarah Meierotto
Kyndall Hildebrandt
Source
Genome. 2017 Mar;60(3):248-259
Date
Mar-2017
Language
English
Publication Type
Article
Keywords
Alaska
Animals
Arthropods - genetics
Biodiversity
Canada
DNA - analysis
DNA Barcoding, Taxonomic - methods
Ecology
Gene Library
Genetic Variation
Geography
Insects - genetics
Models, Genetic
Phylogeny
Sequence Analysis, DNA
Species Specificity
Temperature
Abstract
Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.
PubMed ID
28106469 View in PubMed
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Characterization of genes with increased expression in human glioblastomas.

https://arctichealth.org/en/permalink/ahliterature16547
Source
Tsitol Genet. 2005 Nov-Dec;39(6):37-49
Publication Type
Article
Author
V. Kavsan
K. Shostak
V. Dmitrenko
Yu Zozulya
V. Rozumenko
J. Demotes-Mainard
Author Affiliation
Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine.
Source
Tsitol Genet. 2005 Nov-Dec;39(6):37-49
Language
English
Publication Type
Article
Keywords
Brain - metabolism
Brain Neoplasms - genetics - metabolism
Cell Line, Tumor
Comparative Study
Databases, Genetic
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene Library
Glioblastoma - genetics - metabolism
Humans
Research Support, Non-U.S. Gov't
Tumor Markers, Biological - genetics - metabolism
Abstract
In the present study, we have used the gene expression data available in the SAGE database in an attempt to identify glioblastoma molecular markers. Of 129 genes with more than 5-fold difference found by comparison of nine glioblastoma with five normal brain SAGE libraries, 44 increased their expression in glioblastomas. Most corresponding proteins were involved in angiogenesis, host-tumor immune interplay, multidrug resistance, extracellular matrix (ECM) formation, IGF-signalling, or MAP-kinase pathway. Among them, 16 genes had a high expression both in glioblastomas and in glioblastoma cell lines suggesting their expression in transformed cells. Other 28 genes had an increased expression only in glioblastomas, not in glioblastoma cell lines suggesting an expression possibly originated from host cells. Many of these genes are among the top transcripts in activated macrophages, and involved in immune response and angiogenesis. This altered pattern of gene expression in both host and tumor cells, can be viewed as a molecular marker in the analysis of malignant progression of astrocytic tumors, and as possible clues for the mechanism of disease. Moreover, several genes overexpressed in glioblastomas produce extracellular proteins, thereby providing possible therapeutic targets. Further characterization of these genes will thus allow them to be exploited in molecular classification of glial tumors, diagnosis, prognosis, and anticancer therapy.
PubMed ID
16396319 View in PubMed
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50 records – page 1 of 5.