TY  - JOUR
A1  - Westbury, Michael V.
A1  - Dalerumb, Fredrik
A1  - Noren, Karin
A1  - Hofreiter, Michael
T1  - Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations
JF  - Mitochondrial DNA. Part B
N2  - The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae.
KW  - Phylogenetics
KW  - mitochondria
KW  - iterative mapping
KW  - Canidae
Y1  - 2017
U6  - https://doi.org/10.1080/23802359.2017.1331325
SN  - 2380-2359
VL  - 2
IS  - 1
SP  - 298
EP  - 299
PB  - Routledge, Taylor & Francis Group
CY  - London
ER  - 
TY  - JOUR
A1  - Dolotovskaya, Sofya
A1  - Bordallo, Juan Torroba
A1  - Haus, Tanja
A1  - Noll, Angela
A1  - Hofreiter, Michael
A1  - Zinner, Dietmar
A1  - Roos, Christian
T1  - Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)
JF  - Zoological Journal of the Linnean Society
N2  - Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west-east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested.
KW  - African green monkeys
KW  - baboons
KW  - mitochondrial genomes
KW  - phylogeny
KW  - phylogeography
Y1  - 2017
U6  - https://doi.org/10.1093/zoolinnean/zlx001
SN  - 0024-4082
SN  - 1096-3642
VL  - 181
IS  - 2
SP  - 471
EP  - 483
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Mohandesan, Elmira
A1  - Speller, Camilla F.
A1  - Peters, Joris
A1  - Uerpmann, Hans-Peter
A1  - Uerpmann, Margarethe
A1  - De Cupere, Bea
A1  - Hofreiter, Michael
A1  - Burger, Pamela A.
T1  - Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
JF  - Molecular ecology resources
N2  - The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
KW  - ancient DNA
KW  - Camelus dromedarius
KW  - capture enrichment
KW  - degraded DNA
KW  - mitochondrial genome (mtDNA)
KW  - next-generation sequencing
Y1  - 2017
U6  - https://doi.org/10.1111/1755-0998.12551
SN  - 1755-098X
SN  - 1755-0998
VL  - 17
IS  - 2
SP  - 300
EP  - 313
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Saini, Jeetendra
A1  - Guenther, Franziska
A1  - Aichner, Bernhard
A1  - Mischke, Steffen
A1  - Herzschuh, Ulrike
A1  - Zhang, Chengjun
A1  - Maeusbacher, Roland
A1  - Gleixner, Gerd
T1  - Climate variability in the past similar to 19,000 yr in NE Tibetan Plateau inferred from biomarker and stable isotope records of Lake Donggi Cona
JF  - Quaternary science reviews : the international multidisciplinary research and review journal
N2  - We investigated 4.84-m-long sediment record spanning over the Late Glacial and Holocene from Lake Donggi Cona to be able to reconstruct circulation pattern on the Tibetan Plateau (TP). Presently, Lake Donggi Cona is located at the boundaries of Westerlies and Asian monsoon circulations in the northeastern TP. However, the exact timing and stimulating mechanisms for climatic changes and monsoon shifts in this region are still debated. We used a 19-ka-long stable isotope record of sedimentary n-alkanes to address this discrepancy by providing insights into paleohydrological conditions. The SD of nC(23) is influenced by lake water evaporation; the BD. values of sedimentary nC(29) are mainly controlled by moisture source and temperature changes. Long-chain n-alkanes dominate over the core whereas three mean clusters (i.e. microbial, aquatic and terrestrial) can be inferred. Multi-proxies suggest five major episodes in the history of Lake Donggi Cona. The Lake Donggi Cona record indicates that the Late Glacial(18.4-14.8 cal ka BP) was dominated by low productivity of mainly microbial and aquatic organisms. Relatively low delta D values suggest low temperatures and moist conditions eventually caused by stronger Westerlies, winter monsoon and melt-water influence. Likely, the shift (similar to 17.9 cal ka BP) from microbial to enhanced aquatic input suggests either a change from deep to shallow water lake or a break in local stratification. Between 14.8 and 13.0 cal ka BP, variable climatic conditions prevailed. Although the Westerlies weekend, the increase in temperature enhanced the permafrost and snow melting (displayed by a high sedimentary accumulation rate). Higher delta D values indicate increasingly arid conditions with higher temperatures which eventually lead to high evaporative conditions and lowest lake levels. Low vegetation cover and high erosion rates led to high sediment accumulation resulting in stratification followed by anoxia in the terminal lake. From 13.0 to 9.2 cal ka BP, lowered values of 813 along with high contents of terrestrial organic matter marked the early-Holocene warming indicating a further strengthening of summer precipitation and higher lake levels. A cooling trend was observed in the mid-Holocene between 9.2 and 3.0 cal ka BP accompanied by higher moisture availability (displayed by lowered SD values) caused by reduced evaporative conditions due to a drop in temperature and recovering Westerlies. After 3.0 cal ka BP, a decrease in lake productivity and cold and semi-arid conditions prevailed suggesting lower lake levels and reduced moisture from recycled air masses and Westerlies. We propose that the summer monsoon was the predominant moisture source during the Belling-Allered warm complex and early -Holocene followed by Westerlies in mid-to-late Holocene period. Stable carbon isotope values-32%o indicate the absence of C-4 -type vegetation in the region contradicting with their presence in the Lake Qinghai record. The 81) record from lake Donggi Cona highlights the importance of the interplay between Westerlies and summer monsoon circulation at this location, which is highly dynamic in northeastern plateau compared to the North Atlantic circulation and insolation changes. Consequently lake Donggi Cona might be an important anchor point for environmental reconstructions on the Tibetan Plateau. (C) 2017 The Authors. Published by Elsevier Ltd.
KW  - n-alkanes
KW  - Hydrogen isotopes (delta D)
KW  - Carbon isotopes (delta C-13)
KW  - Carbon preference index (CPI)
KW  - Westerlies
KW  - Continental air masses
KW  - Precipitation
KW  - Late Glacial and Holocene
Y1  - 2017
U6  - https://doi.org/10.1016/j.quascirev.2016.12.023
SN  - 0277-3791
VL  - 157
SP  - 129
EP  - 140
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Weyhenmeyer, Gesa A.
A1  - Mackay, Murray
A1  - Stockwell, Jason D.
A1  - Thiery, Wim
A1  - Grossart, Hans-Peter
A1  - Augusto-Silva, Petala B.
A1  - Baulch, Helen M.
A1  - de Eyto, Elvira
A1  - Hejzlar, Josef
A1  - Kangur, Kuelli
A1  - Kirillin, Georgiy
A1  - Pierson, Don C.
A1  - Rusak, James A.
A1  - Sadro, Steven
A1  - Woolway, R. Iestyn
T1  - Citizen science shows systematic changes in the temperature difference between air and inland waters with global warming
JF  - Scientific reports
N2  - Citizen science projects have a long history in ecological studies. The research usefulness of such projects is dependent on applying simple and standardized methods. Here, we conducted a citizen science project that involved more than 3500 Swedish high school students to examine the temperature difference between surface water and the overlying air (T-w-T-a) as a proxy for sensible heat flux (Q(H)). If Q(H) is directed upward, corresponding to positive T-w-T-a, it can enhance CO2 and CH4 emissions from inland waters, thereby contributing to increased greenhouse gas concentrations in the atmosphere. The students found mostly negative T-w-T-a across small ponds, lakes, streams/rivers and the sea shore (i.e. downward Q(H)), with T-w-T-a becoming increasingly negative with increasing T-a. Further examination of T-w-T-a using high-frequency temperature data from inland waters across the globe confirmed that T-w-T-a is linearly related to T-a. Using the longest available high-frequency temperature time series from Lake Erken, Sweden, we found a rapid increase in the occasions of negative T-w-T-a with increasing annual mean T-a since 1989. From these results, we can expect that ongoing and projected global warming will result in increasingly negative T-w-T-a, thereby reducing CO2 and CH4 transfer velocities from inland waters into the atmosphere.
Y1  - 2017
U6  - https://doi.org/10.1038/srep43890
SN  - 2045-2322
VL  - 7
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Braig, Friederike
A1  - Kriegs, Malte
A1  - Voigtlaender, Minna
A1  - Habel, Beate
A1  - Grob, Tobias
A1  - Biskup, Karina
A1  - Blanchard, Veronique
A1  - Sack, Markus
A1  - Thalhammer, Anja
A1  - Ben Batalla, Isabel
A1  - Braren, Ingke
A1  - Laban, Simon
A1  - Danielczyk, Antje
A1  - Goletz, Steffen
A1  - Jakubowicz, Elzbieta
A1  - Maerkl, Bruno
A1  - Trepel, Martin
A1  - Knecht, Rainald
A1  - Riecken, Kristoffer
A1  - Fehse, Boris
A1  - Loges, Sonja
A1  - Bokemeyer, Carsten
A1  - Binder, Mascha
T1  - Cetuximab Resistance in Head and Neck Cancer Is Mediated by EGFR-K-521 Polymorphism
JF  - Cancer research
N2  - Head and neck squamous cell carcinomas (HNSCC) exhibiting resistance to the EGFR-targeting drug cetuximab poses a challenge to their effective clinical management. Here, we report a specific mechanism of resistance in this setting based upon the presence of a single nucleotide polymorphism encoding EGFR-K-521 (K-allele), which is expressed in > 40% of HNSCC cases. Patients expressing the K-allele showed significantly shorter progressionfree survival upon palliative treatment with cetuximab plus chemotherapy or radiation. In several EGFR-mediated cancer models, cetuximab failed to inhibit downstream signaling or to kill cells harboring a high K-allele frequency. Cetuximab affinity for EGFR-K-521 was reduced slightly, but ligand-mediated EGFR acti-vation was intact. We found a lack of glycan sialyation on EGFR-K-521 that associated with reduced protein stability, suggesting a structural basis for reduced cetuximab efficacy. CetuGEX, an antibody with optimized Fc glycosylation targeting the same epitope as cetuximab, restored HNSCC sensitivity in a manner associated with antibody-dependent cellular cytotoxicity rather than EGFR pathway inhibition. Overall, our results highlight EGFR-K-521 expression as a key mechanism of cetuximab resistance to evaluate prospectively as a predictive biomarker in HNSCC patients. Further, they offer a preclinical rationale for the use of ADCC-optimized antibodies to treat tumors harboring this EGFR isoform.
Y1  - 2017
U6  - https://doi.org/10.1158/0008-5472.CAN-16-0754
SN  - 0008-5472
SN  - 1538-7445
VL  - 77
IS  - 5
SP  - 1188
EP  - 1199
PB  - American Association for Cancer Research
CY  - Philadelphia
ER  - 
TY  - JOUR
A1  - Ietswaart, Robert
A1  - Rosa, Stefanie
A1  - Wu, Zhe
A1  - Dean, Caroline
A1  - Howard, Martin
T1  - Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation
JF  - Cell systems
N2  - Single-cell quantification of transcription kinetics and variability promotes a mechanistic understanding of gene regulation. Here, using single-molecule RNA fluorescence in situ hybridization and mathematical modeling, we dissect cellular RNA dynamics for Arabidopsis FLOWERING LOCUS C (FLC). FLC expression quantitatively determines flowering time and is regulated by antisense (COOLAIR) transcription. In cells without observable COOLAIR expression, we quantify FLC transcription initiation, elongation, intron processing, and lariat degradation, as well as mRNA release from the locus and degradation. In these heterogeneously sized cells, FLC mRNA number increases linearly with cell size, resulting in a large cell-to-cell variability in transcript level. This variation is accounted for by cell-sizedependent, Poissonian FLC mRNA production, but not by large transcriptional bursts. In COOLAIRexpressing cells, however, antisense transcription increases with cell size and contributes to FLC transcription decreasing with cell size. Our analysis therefore reveals an unexpected role for antisense transcription in modulating the scaling of transcription with cell size.
Y1  - 2017
U6  - https://doi.org/10.1016/j.cels.2017.05.010
SN  - 2405-4712
SN  - 2405-4720
VL  - 4
SP  - 622
EP  - 635
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Zibulski, Romy
A1  - Wesener, Felix
A1  - Wilkes, Heinz
A1  - Plessen, Birgit
A1  - Pestryakova, Luidmila Agafyevna
A1  - Herzschuh, Ulrike
T1  - C / N ratio, stable isotope (delta C-13, delta N-15), and n-alkane patterns of brown mosses along hydrological gradients of low-centred polygons of the Siberian Arctic
JF  - Biogeosciences
N2  - Mosses are a major component of the arctic vegetation, particularly in wetlands. We present C / N atomic ratio, delta C-13 and delta N-15 data of 400 brown-moss samples belonging to 10 species that were collected along hydrological gradients within polygonal mires located on the southern Taymyr Peninsula and the Lena River delta in northern Siberia. Additionally, n-alkane patterns of six of these species (16 samples) were investigated. The aim of the study is to see whether the inter-and intraspecific differences in C / N, isotopic compositions and n-alkanes are indicative of habitat, particularly with respect to water level. Overall, we find high variability in all investigated parameters for two different moisture-related groups of moss species. The C / N ratios range between 11 and 53 (median: 32) and show large variations at the intraspecific level. However, species preferring a dry habitat (xero-mesophilic mosses) show higher C / N ratios than those preferring a wet habitat (meso-hygrophilic mosses). The delta C-13 values range between 37.0 and 22.5% (median D 27.8 %). The delta N-15 values range between 6.6 and C 1.7%(median D 2.2 %). We find differences in delta C-13 and delta N-15 compositions between both habitat types. For some species of the meso-hygrophilic group, we suggest that a relationship between the individ-ual habitat water level and isotopic composition can be inferred as a function of microbial symbiosis. The n-alkane distribution also shows differences primarily between xeromesophilic and meso-hygrophilic mosses, i. e. having a dominance of n-alkanes with long (n-C29, n-C31 /and intermediate (n-C25 /chain lengths, respectively. Overall, our results reveal that C / N ratios, isotopic signals and n-alkanes of studied brown-moss taxa from polygonal wetlands are characteristic of their habitat.
Y1  - 2017
U6  - https://doi.org/10.5194/bg-14-1617-2017
SN  - 1726-4170
SN  - 1726-4189
VL  - 14
SP  - 1617
EP  - 1630
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Neumann, Bettina
A1  - Kielb, Patrycja
A1  - Rustam, Lina
A1  - Fischer, Anna
A1  - Weidinger, Inez M.
A1  - Wollenberger, Ulla
T1  - Bioelectrocatalytic Reduction of Hydrogen Peroxide by Microperoxidase-11 Immobilized on Mesoporous Antimony-Doped Tin Oxide
JF  - ChemElectrChem
N2  - The heme-undecapeptide microperoxidase-11 (MP-11) was immobilized on mesoporous antimony-doped tin oxide (ATO) thin-film electrodes modified with the positively charged binding promotor polydiallyldimethylammonium chloride. Surface concentrations of MP-11 of 1.5 nmol cm(-2) were sufficiently high to enable spectroelectrochemical analyses. UV/Vis spectroscopy and resonance Raman spectroscopy revealed that immobilized MP-11 adopts a six-coordinated low-spin conformation, as in solution in the presence of a polycation. Cathodic reduction of hydrogen peroxide at potentials close to +500mV versus Ag/AgCl indicates that the reaction proceeds via a Compound I-type like intermediate, analogous to natural peroxidases, and confirms mesoporous ATO as a suitable host material for adsorbing the heme-peptide in its native state. A hydrogen peroxide sensor is proposed by using the bioelectrocatalytic properties of the MP-11-modified ATO.
KW  - electrochemistry
KW  - enzyme catalysis
KW  - mesoporous materials
KW  - microperoxidase
KW  - spectroelectrochemistry
Y1  - 2017
U6  - https://doi.org/10.1002/celc.201600776
SN  - 2196-0216
VL  - 4
IS  - 4
SP  - 913
EP  - 919
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Meyer, Sebastian Tobias
A1  - Ptacnik, Robert
A1  - Hillebrand, Helmut
A1  - Bessler, Holger
A1  - Buchmann, Nina
A1  - Ebeling, Anne
A1  - Eisenhauer, Nico
A1  - Engels, Christof
A1  - Fischer, Markus
A1  - Halle, Stefan
A1  - Klein, Alexandra-Maria
A1  - Oelmann, Yvonne
A1  - Roscher, Christiane
A1  - Rottstock, Tanja
A1  - Scherber, Christoph
A1  - Scheu, Stefan
A1  - Schmid, Bernhard
A1  - Schulze, Ernst-Detlef
A1  - Temperton, Vicky M.
A1  - Tscharntke, Teja
A1  - Voigt, Winfried
A1  - Weigelt, Alexandra
A1  - Wilcke, Wolfgang
A1  - Weisser, Wolfgang W.
T1  - Biodiversity-multifunctionality relationships depend on identity and number of measured functions
JF  - Nature Ecology & Evolution
N2  - Biodiversity ensures ecosystem functioning and provisioning of ecosystem services, but it remains unclear how biodiversity-ecosystem multifunctionality relationships depend on the identity and number of functions considered. Here, we demonstrate that ecosystem multifunctionality, based on 82 indicator variables of ecosystem functions in a grassland biodiversity experiment, increases strongly with increasing biodiversity. Analysing subsets of functions showed that the effects of biodiversity on multifunctionality were stronger when more functions were included and that the strength of the biodiversity effects depended on the identity of the functions included. Limits to multifunctionality arose from negative correlations among functions and functions that were not correlated with biodiversity. Our findings underline that the management of ecosystems for the protection of biodiversity cannot be replaced by managing for particular ecosystem functions or services and emphasize the need for specific management to protect biodiversity. More plant species from the experimental pool of 60 species contributed to functioning when more functions were considered. An individual contribution to multifunctionality could be demonstrated for only a fraction of the species.
Y1  - 2017
U6  - https://doi.org/10.1038/s41559-017-0391-4
SN  - 2397-334X
VL  - 2
IS  - 1
SP  - 44
EP  - 49
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Bendjeddou, Mohammed Lamine
A1  - Loumassine, Hibat Allah
A1  - Scheffler, Ingo
A1  - Bouslama, Zihad
A1  - Amr, Zuhair
T1  - Bat ectoparasites (Nycteribiidae, Streblidae, Siphonaptera, Heteroptera, Mesostigmata, Argasidae, and Ixodidae) from Algeria
JF  - Journal of Vector Ecology
N2  - Twenty two species of ectoparasites (Family Nycteribiidae: Nycteribia (Listropoda) schmidlii schmidlii, Nycteribia (Nycteribia) latreillii, Nycteribia (Nycteribia) pedicularia, Penicillidia (Penicillidia) dufourii, and Phthiridium biarticulatum; Family Streblidae: Brachytarsina (Brachytarsina) flavipennis and Raymondia huberi; Order Siphonaptera: Rhinolophopsylla unipectinata arabs, Nycteridopsylla longiceps, Araeopsylla gestroi, Ischnopsyllus intermedius, and Ischnopsyllus octactenus; Order Heteroptera: Cimex pipistrelli, Cimex lectularius, and Cacodmus vicinus; Class Arachnida: Order Mesostigmata: Spinturnix myoti and Eyndhovenia euryalis; Order Ixodida: Family Argasidae: Argas transgariepinus and Argas vespertilionis; Family Ixodidae: Hyalomma dromedarii, Ixodes ricinus, and Ixodes vespertilionis) were recovered from 19 bat species in Algeria. New host records for bats are recorded for the first time: N. schmidlii from Rh. clivosus and R. cystops; N. latreillii from Rh. blasii and P. gaisleri; R. huberi from Rh. clivosus; C. pipistrelli from E. isabellinus and H. savii; C. vicinus from E. isabellinus; S. myoti from P. gaisleri; E. euryalis from P. gaisleri and Rh. blasii; A. vespertilionis from P. gaisleri; I. ricinus from T. teniotis and Rh. hipposideros and H. dromedarii from P. kuhlii. Raymondia huberi is recorded for the first time from Algeria.
KW  - Bats
KW  - Nycteribiidae
KW  - Streblidae
KW  - Siphonaptera
KW  - Heteroptera
KW  - Mesostigmata
KW  - Argasidae
KW  - Ixodidae
KW  - Algeria
Y1  - 2017
U6  - https://doi.org/10.1111/jvec.12235
SN  - 1948-7134
VL  - 42
SP  - 13
EP  - 23
PB  - Wiley Interscience
CY  - Hoboken, NJ
ER  - 
TY  - JOUR
A1  - Leimkühler, Silke
A1  - Lemaire, Olivier N.
A1  - Iobbi-Nivol, Chantal
T1  - Bacterial Molybdoenzymes
BT  - Chaperones, Assembly and Insertion
JF  - Molybdenum and tungsten enzymes : biochemistry
N2  - The biogenesis of molybdoenzymes is a cytoplasmic event requiring both the folded apoenzymes and the matured molybdenum cofactor. The structure and the complexity of the molybdenum cofactor varies in each molybdoenzyme family and consequently different accessory proteins are required for the maturation of the respective enzymes. Thus, for enzymes of both the DMSO reductase and xanthine oxidase families, specific chaperones exist which are dedicated to increase the stability and the folding of specific members of each family. In this review, we describe the role of these chaperones for molybdoenzyme maturation. We present a model which describes step by step the mechanism of the maturation of representative molybdoenzymes from each family.
Y1  - 2016
SN  - 978-1-78262-391-5
SN  - 978-1-78262-089-1
U6  - https://doi.org/10.1039/9781782623915-00117
VL  - 5
SP  - 117
EP  - 142
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Nakamura, Moritaka
A1  - Claes, Andrea R.
A1  - Grebe, Tobias
A1  - Hermkes, Rebecca
A1  - Viotti, Corrado
A1  - Ikeda, Yoshihisa
A1  - Grebe, Markus
T1  - Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - Polar nuclear migration is crucial during the development of diverse eukaryotes. In plants, root hair growth requires polar nuclear migration into the outgrowing hair. However, knowledge about the dynamics and the regulatory mechanisms underlying nuclear movements in root epidermal cells remains limited. Here, we show that both auxin and Rho-of-Plant (ROP) signaling modulate polar nuclear position at the inner epidermal plasma membrane domain oriented to the cortical cells during cell elongation as well as subsequent polar nuclear movement to the outer domain into the emerging hair bulge in Arabidopsis (Arabidopsis thaliana). Auxin signaling via the nuclear AUXIN RESPONSE FACTOR7 (ARF7)/ARF19 and INDOLE ACETIC ACID7 pathway ensures correct nuclear placement toward the inner membrane domain. Moreover, precise inner nuclear placement relies on SPIKE1 Rho-GEF, SUPERCENTIPEDE1 Rho-GDI, and ACTIN7 (ACT7) function and to a lesser extent on VTI11 vacuolar SNARE activity. Strikingly, the directionality and/or velocity of outer polar nuclear migration into the hair outgrowth along actin strands also are ACT7 dependent, auxin sensitive, and regulated by ROP signaling. Thus, our findings provide a founding framework revealing auxin and ROP signaling of inner polar nuclear position with some contribution by vacuolar morphology and of actin-dependent outer polar nuclear migration in root epidermal hair cells.
Y1  - 2017
U6  - https://doi.org/10.1104/pp.17.00713
SN  - 0032-0889
SN  - 1532-2548
VL  - 176
IS  - 1
SP  - 378
EP  - 391
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Shahnejat-Bushehri, Sara
A1  - Allu, Annapurna Devi
A1  - Mehterov, Nikolay
A1  - Thirumalaikumar, Venkatesh P.
A1  - Alseekh, Saleh
A1  - Fernie, Alisdair R.
A1  - Mueller-Roeber, Bernd
A1  - Balazadeh, Salma
T1  - Arabidopsis NAC Transcription Factor JUNGBRUNNEN1 Exerts Conserved Control Over Gibberellin and Brassinosteroid Metabolism and Signaling Genes in Tomato
JF  - Frontiers in plant science
N2  - The Arabidopsis thaliana NAC transcription factor JUNGBRUNNEN1 (AtJUB1) regulates growth by directly repressing GA3ox1 and DWF4, two key genes involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis, respectively, leading to GA and BR deficiency phenotypes. AtJUB1 also reduces the expression of PIF4, a bHLH transcription factor that positively controls cell elongation, while it stimulates the expression of DELLA genes, which are important repressors of growth. Here, we extend our previous findings by demonstrating that AtJUB1 induces similar GA and BR deficiency phenotypes and changes in gene expression when overexpressed in tomato (Solanum lycopersicum). Importantly, and in accordance with the growth phenotypes observed, AtJUB1 inhibits the expression of growth-supporting genes, namely the tomato orthologs of GA3ox1, DWF4 and PIF4, but activates the expression of DELLA orthologs, by directly binding to their promoters. Overexpression of AtJUB1 in tomato delays fruit ripening, which is accompanied by reduced expression of several ripeningrelated genes, and leads to an increase in the levels of various amino acids (mostly proline, beta-alanine, and phenylalanine), gamma-aminobutyric acid (GABA), and major organic acids including glutamic acid and aspartic acid. The fact that AtJUB1 exerts an inhibitory effect on the GA/BR biosynthesis and PIF4 genes but acts as a direct activator of DELLA genes in both, Arabidopsis and tomato, strongly supports the model that the molecular constituents of the JUNGBRUNNEN1 growth control module are considerably conserved across species.
KW  - Arabidopsis
KW  - tomato
KW  - fruit
KW  - growth
KW  - transcription factor
KW  - gibberellic acid
KW  - brassinosteroid
KW  - DELLA proteins
Y1  - 2017
U6  - https://doi.org/10.3389/fpls.2017.00214
SN  - 1664-462X
VL  - 8
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Kang, Mi-Sun
A1  - Lim, Hae-Soon
A1  - Oh, Jong-Suk
A1  - Lim, You-jin
A1  - Wuertz-Kozak, Karin
A1  - Harro, Janette M.
A1  - Shirtliff, Mark E.
A1  - Achermann, Yvonne
T1  - Antimicrobial activity of Lactobacillus salivarius and Lactobacillus fermentum against Staphylococcus aureus
JF  - Pathogens and disease / Federation of European Microbiology Societies
N2  - The increasing prevalence of methicillin-resistant Staphylococcus aureus has become a major public health threat. While lactobacilli were recently found useful in combating various pathogens, limited data exist on their therapeutic potential for S. aureus infections. The aim of this study was to determine whether Lactobacillus salivarius was able to produce bactericidal activities against S. aureus and to determine whether the inhibition was due to a generalized reduction in pH or due to secreted Lactobacillus product(s). We found an 8.6-log10 reduction of planktonic and a 6.3-log10 reduction of biofilm S. aureus. In contrast, the previously described anti-staphylococcal effects of L. fermentum only caused a 4.0-log10 reduction in planktonic S. aureus cells, with no effect on biofilm S. aureus cells. Killing of S. aureus was partially pH dependent, but independent of nutrient depletion. Cell-free supernatant that was pH neutralized and heat inactivated or proteinase K treated had significantly reduced killing of L. salivarius than with pH-neutralized supernatant alone. Proteomic analysis of the L. salivarius secretome identified a total of five secreted proteins including a LysM-containing peptidoglycan binding protein and a protein peptidase M23B. These proteins may represent potential novel anti-staphylococcal agents that could be effective against S. aureus biofilms.
KW  - antibacterial activity
KW  - biofilm
KW  - Lactobacillus fermentum
KW  - Lactobacillus salivarius
KW  - LysM
KW  - Staphylococcus aureus
Y1  - 2017
U6  - https://doi.org/10.1093/femspd/ftx009
SN  - 2049-632X
VL  - 75
IS  - 2
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Czernitzki, Anna-Franziska
A1  - Pospisil, Christina
A1  - Musalek, Martin
A1  - Mumm, Rebekka
A1  - Scheffler, Christiane
T1  - Analysis of longitudinal data of height z-scores in kindergarten children
BT  - a pilot study
JF  - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie
N2  - Changes in body height throughout extended historic periods are very complex and dynamic processes. Thispilot study aimed to investigate the pattern of longitudinal height z-scores changes in children before and after entering kindergarten. In summer 2016, we measured height and weight of 32 children from 4 groups of two kindergartens aged 3–6 years. All ages were centered according to the age of entry into the kindergarten. For each child we determined mean z-scores for height before and after entering the kindergarten, and assessed the variances for each kindergarten group. Twenty-two children targeted in height z-scores towards average height of their respective kindergarten group, 10 children did not. Due to the small numbers, the convergence in height variance however, remained insignificant (chi-squared independence test, p = 0.127). Additional studies with larger sample sizes are needed to confirm this pilot study.
KW  - Height z-score
KW  - kindergarten children
KW  - secular trend
KW  - strategic growth adjustment
KW  - social signal
Y1  - 2017
U6  - https://doi.org/10.1127/anthranz/2017/0708
SN  - 0003-5548
VL  - 74
IS  - 2
SP  - 109
EP  - 112
PB  - Schweizerbart science publishers
CY  - Stuttgart
ER  - 
TY  - JOUR
A1  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Martin, Michael D.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Rawlence, Nicolas J.
A1  - Fuller, Errol
A1  - Fjeldsa, Jon
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - An ‛Aukward’ tale
BT  - a genetic approach to discover the whereabouts of the  Last Great Auks
JF  - Genes
N2  - One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.
KW  - ancient DNA
KW  - extinct birds
KW  - mitochondrial genome
KW  - museum specimens
KW  - palaeogenomics
Y1  - 2017
U6  - https://doi.org/10.3390/genes8060164
SN  - 2073-4425
VL  - 8
IS  - 6
SP  - 164
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Salleh, Faezah Mohd
A1  - Ramos-Madrigal, Jazmin
A1  - Penaloza, Fernando
A1  - Liu, Shanlin
A1  - Sinding, Mikkel-Holger S.
A1  - Patel, Riddhi P.
A1  - Martins, Renata
A1  - Lenz, Dorina
A1  - Fickel, Jörns
A1  - Roos, Christian
A1  - Shamsir, Mohd Shahir
A1  - Azman, Mohammad Shahfiz
A1  - Lim, Burton K.
A1  - Rossiter, Stephen J.
A1  - Wilting, Andreas
A1  - Gilbert, M. Thomas P.
T1  - An expanded mammal mitogenome dataset from Southeast Asia
JF  - Gigascience
N2  - Background: Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion:
KW  - invertebrate-derived (iDNA)
KW  - metabarcoding
KW  - GenBank
KW  - Taxonomic assignment
Y1  - 2017
SN  - 2047-217X
VL  - 6
IS  - 8
SP  - 1
EP  - 19
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Fischbach, Jens
A1  - Loh, Qiuting
A1  - Bier, Frank Fabian
A1  - Lim, Theam Soon
A1  - Frohme, Marcus
A1  - Glökler, Jörn
T1  - Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method
JF  - Scientific reports
N2  - We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.
Y1  - 2017
U6  - https://doi.org/10.1038/srep45085
SN  - 2045-2322
VL  - 7
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Heunisch, Fabian
A1  - Chaykovska, Lyubov
A1  - von Einem, Gina
A1  - Alter, Markus
A1  - Dschietzig, Thomas
A1  - Kretschmer, Axel
A1  - Kellner, Karl-Heinz
A1  - Hocher, Berthold
T1  - ADMA predicts major adverse renal events in patients with mild renal impairment and/or diabetes mellitus undergoing coronary angiography
JF  - Medicine
N2  - Asymmetric dimethylarginine (ADMA) is a competitive inhibitor of the nitric oxide (NO)-synthase and a biomarker of endothelial dysfunction (ED). ED plays an important role in the pathogenesis of contrast-induced nephropathy (CIN). The aim of our study was to evaluate serum ADMA concentration as a biomarker of an acute renal damage during the follow-up of 90 days after contrast medium (CM) application. Blood samples were obtained from 330 consecutive patients with diabetes mellitus or mild renal impairment immediately before, 24 and 48 hours after the CM application for coronary angiography. The patients were followed for 90 days. The composite endpoints were major adverse renal events (MARE) defined as occurrence of death, initiation of dialysis, or a doubling of serum creatinine concentration. Overall, ADMA concentration in plasma increased after CM application, although, there was no differences between ADMA levels in patients with and without CIN. ADMA concentration 24 hours after the CM application was predictive for dialysis with a specificity of 0.889 and sensitivity of 0.653 at values higher than 0.71 mu mol/L (area under the curve: 0.854, 95% confidential interval: 0.767-0.941, P<0.001). This association remained significant in multivariate Cox regression models adjusted for relevant factors of long-term renal outcome. 24 hours after the CM application, ADMA concentration in plasma was predictive for MARE with a specificity of 0.833 and sensitivity of 0.636 at a value of more than 0.70 mu mol/L (area under the curve: 0.750, 95% confidence interval: 0.602-0.897, P=0.004). Multivariate logistic regression analysis confirmed that ADMA and anemia were significant predictors of MARE. Further analysis revealed that increased ADMA concentration in plasma was highly significant predictor of MARE in patients with CIN. Moreover, patients with CIN and MARE had the highest plasma ADMA levels 24 hours after CM exposure in our study cohort. The impact of ADMA on MARE was independent of such known CIN risk factors as anemia, pre-existing renal failure, pre-existing heart failure, and diabetes. ADMA concentration in plasma is a promising novel biomarker of major contrast-induced nephropathy-associated events 90 days after contrast media exposure.
KW  - asymmetric dimethylarginine (ADMA)
KW  - biomarkers of renal failure
KW  - contrast-induced nephropathy
Y1  - 2017
U6  - https://doi.org/10.1097/MD.0000000000006065
SN  - 0025-7974
SN  - 1536-5964
VL  - 96
IS  - 6
PB  - Lippincott Williams & Wilkins
CY  - Philadelphia
ER  -