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Selection against tandem splice sites affecting structured protein regions

Hiller, Michael ; Szafranski, Karol ; Huse, Klaus ; [et al.]

Springer Science and Business Media LLC ; 2008

In: BMC Evolutionary Biology Vol. 8, No. 1 ( 2008), p. 89-

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In: BMC Evolutionary Biology, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2008), p. 89-

Type of Medium: Online Resource

ISSN: 1471-2148

URL: Article

DOI: 10.1186/1471-2148-8-89

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2008

detail.hit.zdb_id: 2041493-6

detail.hit.zdb_id: 3053924-9

SSG: 12

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High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

Reichwald, Kathrin ; Lauber, Chris ; Nanda, Indrajit ; [et al.]

Springer Science and Business Media LLC ; 2009

In: Genome Biology Vol. 10, No. 2 ( 2009), p. R16-

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In: Genome Biology, Springer Science and Business Media LLC, Vol. 10, No. 2 ( 2009), p. R16-

Type of Medium: Online Resource

ISSN: 1465-6906

URL: Article

DOI: 10.1186/gb-2009-10-2-r16

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2009

detail.hit.zdb_id: 2040529-7

SSG: 12

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tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression

Szafranski, Karol ; Jahn, Niels ; Platzer, Matthias

Oxford University Press (OUP) ; 2006

In: Bioinformatics Vol. 22, No. 15 ( 2006-08-01), p. 1917-1918

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In: Bioinformatics, Oxford University Press (OUP), Vol. 22, No. 15 ( 2006-08-01), p. 1917-1918

Abstract: Summary: The program tuple_plot identifies and visualizes local similarities between two genomic sequences, typically 100 kb or longer, by applying the well-known dotplot principle. A dictionary of sequence words built from the input sequences serves to construct a task-specific expectancy model that is used to attribute significance values to pairwise word hits. The dictionary-based approach allows fast computation, the computation time scaling to O(N log N), depending on the size of the input sequences. The proposed scoring scheme appreciably increases the signal-to-noise ratio and may help to improve other word-based sequence comparison approaches. Availability: tuple_plot is available at and may be used under GNU public license. Contact: szafrans@fli-leibniz.de

Type of Medium: Online Resource

ISSN: 1367-4811 , 1367-4803

URL: Article

DOI: 10.1093/bioinformatics/btl277

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2006

detail.hit.zdb_id: 1468345-3

SSG: 12

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Transkriptom-Sequenzierung in der Alternsforschung : Biologie des Alterns

Groth, Marco ; Reichwald, Kathrin ; Szafranski, Karol ; [et al.]

Springer Science and Business Media LLC ; 2014

In: BIOspektrum Vol. 20, No. 2 ( 2014-3), p. 163-166

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In: BIOspektrum, Springer Science and Business Media LLC, Vol. 20, No. 2 ( 2014-3), p. 163-166

Type of Medium: Online Resource

ISSN: 0947-0867 , 1868-6249

URL: Article

DOI: 10.1007/s12268-014-0423-4

Language: German

Publisher: Springer Science and Business Media LLC

Publication Date: 2014

detail.hit.zdb_id: 1236314-5

detail.hit.zdb_id: 2203536-9

SSG: 12

SSG: 15,3

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Abundance and size of hyaluronan in naked mole-rat tissues and plasma

del Marmol, Delphine ; Holtze, Susanne ; Kichler, Nadia ; [et al.]

Springer Science and Business Media LLC ; 2021

In: Scientific Reports Vol. 11, No. 1 ( 2021-04-12)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-04-12)

Abstract: Large amounts of ultra-high molecular weight hyaluronan (HA) have been described as the main cause of cancer resistance in naked mole-rats ( Heterocephalus glaber , NMR). Our work examined HA metabolism in these rodents more closely. HA was localized and quantified using HA binding proteins. Its molecular weight was determined using size exclusion chromatography and gel electrophoresis, HA family gene expression using RNAseq analysis, and hyaluronidase activity using zymography. Guinea pigs ( Cavia porcellus ) and mice ( Mus musculus ) were used as controls for some experiments. We found that HA localization was similar in NMR, guinea pig, and mouse tissues but NMR had larger amounts and higher molecular weight (maximum, around 2.5 MDa) of HA in serum and almost all tissues tested. We could not find ultra-high molecular weight HA (≥ 4 MDa) in NMR samples, in contrast to previous descriptions. Hyaluronidase-1 had lower expression and activity in NMR than mouse lymph nodes. RNAseq results showed that, among HA family genes, Tnfaip6 and hyaluronidase-3 ( Hyal3 ) were systematically overexpressed in NMR tissues. In conclusion, NMR samples, contrary to expectations, do not harbor ultra-high molecular weight HA, although its amount and average molecular weight are higher in NMR than in guinea pig tissues and serum. Although hyaluronidase expression and activity are lower in NMR than mouse lymph nodes, this not sufficient to explain the presence of high molecular weight HA. A different activity of the NMR HA synthases remains possible. These characteristics, together with extremely high Hyal3 and Tnfaip6 expression, may provide the NMR with a bespoke, and perhaps protective, HA metabolism.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-021-86967-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2021

detail.hit.zdb_id: 2615211-3

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Common Determinants of Credit Default Swap Premia in the North American Oil and Gas Industry. A Panel BMA Approach

Szafranek, Karol ; Kwas, Marek ; Szafrański, Grzegorz ; [et al.]

MDPI AG ; 2020

In: Energies Vol. 13, No. 23 ( 2020-11-30), p. 6327-

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In: Energies, MDPI AG, Vol. 13, No. 23 ( 2020-11-30), p. 6327-

Abstract: This study discovered market determinants of credit default swap (CDS) spreads in the North American oil and gas industry. Due to the limited theoretical background on market sources of CDS price fluctuations, we chose to alleviate model uncertainty and possible misspecification issues using Bayesian model averaging. This robust framework allowed us to aggregate results from a vast number of linear panel models estimated over the 2017–2020 period. We identified oil price volatility, major shifts in the OPEC+ supply policy, natural gas prices and industrial metal prices as the most robust determinants of CDS spreads. We show that following the onset of the COVID-19 pandemic, oil prices ceased to be a notably important determinant of credit risk, as factors indirectly related to oil prices, such as global and sectoral uncertainty, financial conditions and the macroeconomic stance became more influential. Additionally, we show that the CDS spreads of shale companies are determined by similar common factors, but they are more sensitive to the OPEC+ decisions on the global supply and are less affected by the domestic activity. Finally, we also prove that our modelling approach may help investors and risk officers to identify robust determinants behind the dynamics of credit risk.

Type of Medium: Online Resource

ISSN: 1996-1073

URL: Article

DOI: 10.3390/en13236327

Language: English

Publisher: MDPI AG

Publication Date: 2020

detail.hit.zdb_id: 2437446-5

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Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

Fritsch, Claudia ; Herrmann, Alexander ; Nothnagel, Michael ; [et al.]

Cold Spring Harbor Laboratory ; 2012

In: Genome Research Vol. 22, No. 11 ( 2012-11), p. 2208-2218

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In: Genome Research, Cold Spring Harbor Laboratory, Vol. 22, No. 11 ( 2012-11), p. 2208-2218

Abstract: So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was trained on the ribosomal footprints observed at previously annotated AUG translation initiation codons (TICs), and used for the ab initio prediction of TISs in 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) in the 5′ UTR, 1406 uORFs overlapping with the coding sequence, and 546 N-terminal protein extensions. The TIS detection method was validated on the basis of previously published alternative TISs and uORFs. Among primates, TICs in newly annotated TISs were significantly more conserved than control codons, both for AUGs and near-cognate codons. The transcriptome-wide map of novel candidate TISs derived as part of the study will shed further light on the way in which human proteome diversity is influenced by alternative translation initiation and regulation.

Type of Medium: Online Resource

ISSN: 1088-9051

URL: Article

DOI: 10.1101/gr.139568.112

RVK:

XA 10000

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2012

detail.hit.zdb_id: 1483456-X

SSG: 12

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Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?

Platzer, Matthias ; Hiller, Michael ; Szafranski, Karol ; [et al.]

Springer Science and Business Media LLC ; 2006

In: Nature Biotechnology Vol. 24, No. 9 ( 2006-09-01), p. 1068-1070

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In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 24, No. 9 ( 2006-09-01), p. 1068-1070

Type of Medium: Online Resource

ISSN: 1087-0156 , 1546-1696

URL: Article

DOI: 10.1038/nbt0906-1068b

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2006

detail.hit.zdb_id: 1494943-X

detail.hit.zdb_id: 1311932-1

SSG: 12

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Hematologic adaptation to the subterranean environment by the naked mole-rat, Heterocephalus glaber (Ctenohystrica: Heterocephalidae)

Holtze, Susanne ; Koch, Rosie ; Hildebrandt, Thomas Bernd ; [et al.]

Oxford University Press (OUP) ; 2020

In: Journal of Mammalogy Vol. 101, No. 4 ( 2020-09-09), p. 1000-1009

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In: Journal of Mammalogy, Oxford University Press (OUP), Vol. 101, No. 4 ( 2020-09-09), p. 1000-1009

Abstract: One method burrowing animals are hypothesized to use in adapting to the presumed hypoxic subterranean environment is increasing the oxygen-carrying capacity of blood. A number of recent studies have examined hematologic parameters in laboratory-reared naked mole-rats, but not in animals living under natural atmospheric conditions. To our knowledge, blood chemistry parameters have never been systematically assessed in a fossorial mammal. In this study we examined the blood of wild naked mole-rats in Kenya and Ethiopia to determine whether their blood chemistry differs significantly from naked mole-rats born and living in captivity. We also compared our results to published values for hystricomorphs, other subterranean rodents, and surface-dwelling rodents of similar size.

Type of Medium: Online Resource

ISSN: 0022-2372 , 1545-1542

URL: Article

DOI: 10.1093/jmammal/gyaa053

RVK:

WA 15000

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2020

detail.hit.zdb_id: 2066602-0

SSG: 12

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Unusual Ratio between Free Thyroxine and Free Triiodothyronine in a Long-Lived Mole-Rat Species with Bimodal Ageing

Henning, Yoshiyuki ; Vole, Christiane ; Begall, Sabine ; [et al.]

Public Library of Science (PLoS) ; 2014

In: PLoS ONE Vol. 9, No. 11 ( 2014-11-19), p. e113698-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 9, No. 11 ( 2014-11-19), p. e113698-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0113698

DOI: 10.1371/journal.pone.0113698.g001

DOI: 10.1371/journal.pone.0113698.g002

DOI: 10.1371/journal.pone.0113698.g003

DOI: 10.1371/journal.pone.0113698.g004

DOI: 10.1371/journal.pone.0113698.t001

DOI: 10.1371/journal.pone.0113698.t002

DOI: 10.1371/journal.pone.0113698.t003

DOI: 10.1371/journal.pone.0113698.t004

DOI: 10.1371/journal.pone.0113698.s001

DOI: 10.1371/journal.pone.0113698.s002

DOI: 10.1371/journal.pone.0113698.s003

DOI: 10.1371/journal.pone.0113698.s004

DOI: 10.1371/journal.pone.0113698.s005

DOI: 10.1371/journal.pone.0113698.s006

DOI: 10.1371/journal.pone.0113698.s007

DOI: 10.1371/journal.pone.0113698.s008

DOI: 10.1371/journal.pone.0113698.s009

DOI: 10.1371/journal.pone.0113698.s010

DOI: 10.1371/journal.pone.0113698.s011

DOI: 10.1371/journal.pone.0113698.s012

DOI: 10.1371/journal.pone.0113698.s013

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2014

detail.hit.zdb_id: 2267670-3

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