TY  - JOUR
A1  - Wurzbacher, Christian
A1  - Warthmann, Norman
A1  - Bourne, Elizabeth Charlotte
A1  - Attermeyer, Katrin
A1  - Allgaier, Martin
A1  - Powell, Jeff R.
A1  - Detering, Harald
A1  - Mbedi, Susan
A1  - Grossart, Hans-Peter
A1  - Monaghan, Michael T.
T1  - High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)
JF  - MycoKeys
N2  - Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.
KW  - Freshwater fungi
KW  - aquatic fungi
KW  - metabarcoding
KW  - LSU
KW  - GMYC
KW  - habitat specificity
KW  - Chytridiomycota
KW  - Cryptomycota
KW  - Rozellomycota
KW  - community ecology
KW  - lake ecosystem
KW  - biofilm
KW  - sediment
KW  - plankton
KW  - water sample
KW  - benthos
KW  - reed
KW  - fungal diversity
Y1  - 2016
U6  - https://doi.org/10.3897/mycokeys.16.9646
SN  - 1314-4057
SN  - 1314-4049
VL  - 41
SP  - 17
EP  - 44
PB  - Pensoft Publ.
CY  - Sofia
ER  - 
TY  - JOUR
A1  - Vences, Miguel
A1  - Lyra, Mariana L.
A1  - Kueneman, Jordan G.
A1  - Bletz, Molly C.
A1  - Archer, Holly M.
A1  - Canitz, Julia
A1  - Handreck, Svenja
A1  - Randrianiaina, Roger-Daniel
A1  - Struck, Ulrich
A1  - Bhuju, Sabin
A1  - Jarek, Michael
A1  - Geffers, Robert
A1  - McKenzie, Valerie J.
A1  - Tebbe, Christoph C.
A1  - Haddad, CLio F. B.
A1  - Glos, Julian
T1  - Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas
JF  - The science of nature
N2  - Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.
KW  - Amphibia
KW  - Anura
KW  - Tadpoles
KW  - Gutmicrobiota
KW  - 16S rRNA
KW  - Stable isotopes
Y1  - 2016
U6  - https://doi.org/10.1007/s00114-016-1348-1
SN  - 0028-1042
SN  - 1432-1904
VL  - 103
SP  - 68
EP  - 73
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Lehmann, Andreas
A1  - Scheffler, Christiane
T1  - What does the mean menarcheal age mean?An analysis of temporal pattern in variability in a historical swiss population from the 19th and 20th centuries
JF  - American journal of human biology : the official journal of the Human Biology Council
N2  - ObjectivesAge at menarche is one of the most important factors when observing growth and development. The aim of this study was to assess the temporal pattern in variability of menarcheal age for a historic Swiss population from the 19th and 20th centuries. ResultsMean menarcheal age declined from 17.34 years (n=358) around 1830 to 13.80 years (n=141) around 1950. Within-cohort variance decreased from 7.5 to 2.1 year(2). Skewness was negatively correlated with birth year (r=-0.58). ConclusionThis study provided evidence for a secular trend in various statistical parameters for age at menarche since the 19th century. Furthermore, the results of the analysis of temporal pattern in variability revealed that the secular trend in menarcheal age happened in two phases. Am. J. Hum. Biol. 28:705-713, 2016. (c) 2016 Wiley Periodicals, Inc.
Y1  - 2016
U6  - https://doi.org/10.1002/ajhb.22854
SN  - 1042-0533
SN  - 1520-6300
VL  - 28
SP  - 705
EP  - 713
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Cui, Pin
A1  - Löber, Ulrike
A1  - Alquezar-Planas, David E.
A1  - Ishida, Yasuko
A1  - Courtiol, Alexandre
A1  - Timms, Peter
A1  - Johnson, Rebecca N.
A1  - Lenz, Dorina
A1  - Helgen, Kristofer M.
A1  - Roca, Alfred L.
A1  - Hartman, Stefanie
A1  - Greenwood, Alex D.
T1  - Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome
JF  - PeerJ
N2  - Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.
KW  - Integration sites
KW  - Retroviral endogenization
KW  - KoRV
KW  - Target enrichment
KW  - Clustering
Y1  - 2016
U6  - https://doi.org/10.7717/peerj.1847
SN  - 2167-8359
VL  - 4
PB  - PeerJ Inc.
CY  - London
ER  - 
TY  - JOUR
A1  - Czesnick, Hjördis
A1  - Lenhard, Michael
T1  - Antagonistic control of flowering time by functionally specialized poly(A) polymerases in Arabidopsis thaliana
JF  - The plant journal
N2  - Polyadenylation is a critical 3-end processing step during maturation of pre-mRNAs, and the length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerase (PAPS) isoforms fulfilling specialized functions, as reflected by their different mutant phenotypes. While PAPS1 affects several processes, such as the immune response, organ growth and male gametophyte development, the roles of PAPS2 and PAPS4 are largely unknown. Here we demonstrate that PAPS2 and PAPS4 promote flowering in a partially redundant manner. The enzymes act antagonistically to PAPS1, which delays the transition to flowering. The opposite flowering-time phenotypes in paps1 and paps2 paps4 mutants are at least partly due to decreased or increased FLC activity, respectively. In contrast to paps2 paps4 mutants, plants with increased PAPS4 activity flower earlier than the wild-type, concomitant with reduced FLC expression. Double mutant analyses suggest that PAPS2 and PAPS4 act independently of the autonomous pathway components FCA, FY and CstF64. The direct polyadenylation targets of the three PAPS isoforms that mediate their effects on flowering time do not include FLC sense mRNA and remain to be identified. Thus, our results uncover a role for canonical PAPS isoforms in flowering-time control, raising the possibility that modulating the balance of the isoform activities could be used to fine tune the transition to flowering. Significance Statement The length of the poly(A) tail affects mRNA stability, nuclear export and translation efficiency. Arabidopsis has three isoforms of nuclear poly(A) polymerase (PAPS): PAPS1 plays a major role in organ growth and plant defence. Here we show that PAPS2 and PAPS4 redundantly promote flowering and act antagonistically to PAPS1, which delays flowering. We suggest that modulating the activity of these isoforms fine-tunes the transition to flowering.
KW  - polyadenylation
KW  - 3-end processing
KW  - poly(A) polymerase
KW  - flowering time
KW  - autonomous pathway
KW  - Arabidopsis thaliana
Y1  - 2016
U6  - https://doi.org/10.1111/tpj.13280
SN  - 0960-7412
SN  - 1365-313X
VL  - 88
SP  - 570
EP  - 583
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Jöst, Moritz
A1  - Hensel, Goetz
A1  - Kappel, Christian
A1  - Druka, Arnis
A1  - Sicard, Adrien
A1  - Hohmann, Uwe
A1  - Beier, Sebastian
A1  - Himmelbach, Axel
A1  - Waugh, Robbie
A1  - Kumlehn, Jochen
A1  - Stein, Nils
A1  - Lenhard, Michael
T1  - The INDETERMINATE DOMAIN Protein BROAD LEAF1 Limits Barley Leaf Width by Restricting Lateral Proliferation
JF  - Current biology
N2  - Variation in the size, shape, and positioning of leaves as the major photosynthetic organs strongly impacts crop yield, and optimizing these aspects is a central aim of cereal breeding [1, 2]. Leaf growth in grasses is driven by cell proliferation and cell expansion in a basal growth zone [3]. Although several factors influencing final leaf size and shape have been identified from rice and maize [4-14], what limits grass leaf growth in the longitudinal or transverse directions during leaf development remains poorly understood. To identify factors involved in this process, we characterized the barley mutant broad leaf1 (blf1). Mutants form wider but slightly shorter leaves due to changes in the numbers of longitudinal cell files and of cells along the leaf length. These differences arise during primordia outgrowth because of more cell divisions in the width direction increasing the number of cell files. Positional cloning, analysis of independent alleles, and transgenic complementation confirm that BLF1 encodes a presumed transcriptional regulator of the INDETERMINATE DOMAIN family. In contrast to loss-of-function mutants, moderate overexpression of BLF1 decreases leaf width below wild-type levels. A functional BLF1-vYFP fusion protein expressed from the endogenous promoter shows a dynamic expression pattern in the shoot apical meristem and young leaf primordia. Thus, we propose that the BLF1 gene regulates barley leaf size by restricting cell proliferation in the leaf-width direction. Given the agronomic importance of canopy traits in cereals, identifying functionally different BLF1 alleles promises to allow for the generation of optimized cereal ideotypes.
Y1  - 2016
U6  - https://doi.org/10.1016/j.cub.2016.01.047
SN  - 0960-9822
SN  - 1879-0445
VL  - 26
SP  - 903
EP  - 909
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Sicard, Adrien
A1  - Kappel, Christian
A1  - Lee, Young Wha
A1  - Wozniak, Natalia Joanna
A1  - Marona, Cindy
A1  - Stinchcombe, John R.
A1  - Wright, Stephen I.
A1  - Lenhard, Michael
T1  - Standing genetic variation in a tissue-specific enhancer underlies
selfing-syndrome evolution in Capsella
JF  - Proceedings of the National Academy of Sciences of the United States of America
N2  - Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such as size, evolve are poorly understood. In particular, it is unclear how natural selection can specifically modulate the size of one organ despite the pleiotropic action of most known growth regulators. Here, we demonstrate that allelic variation in the intron of a general growth regulator contributed to the specific reduction of petal size after the transition to selfing in the genus Capsella. Variation within this intron affects an organ-specific enhancer that regulates the level of STERILE APETALA (SAP) protein in the developing petals. The resulting decrease in SAP activity leads to a shortening of the cell proliferation period and reduced number of petal cells. The absence of private polymorphisms at the causal region in the selfing species suggests that the small-petal allele was captured from standing genetic variation in the ancestral out-crossing population. Petal-size variation in the current out-crossing population indicates that several small-effect mutations have contributed to reduce petal-size. These data demonstrate how tissue-specific regulatory elements in pleiotropic genes contribute to organ-specific evolution. In addition, they provide a plausible evolutionary explanation for the rapid evolution of flower size after the out-breeding-to-selfing transition based on additive effects of segregating alleles.
KW  - morphological evolution
KW  - growth control
KW  - standing variation;
 organ-specific evolution
KW  - intronic cis-regulatory element
Y1  - 2016
U6  - https://doi.org/10.1073/pnas.1613394113
SN  - 0027-8424
VL  - 113
SP  - 13911
EP  - 13916
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Ronquillo, Cecinio C.
A1  - Hanke-Gogokhia, Christin
A1  - Revelo, Monica P.
A1  - Frederick, Jeanne M.
A1  - Jiang, Li
A1  - Baehr, Wolfgang
T1  - Ciliopathy-associated IQCB1/NPHP5 protein is required for mouse photoreceptor outer segment formation
JF  - The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology
N2  - Null mutations in the human IQCB1/NPHP5 (nephrocystin-5) gene that encodes NPHP5 are the most frequent cause of Senior-LOken syndrome, a ciliopathy that is characterized by Leber congenital amaurosis and nephronophthisis. We generated germline Nphp5-knockout mice by placing a -Geo gene trap in intron 4, thereby truncating NPHP5 at Leu87 and removing all known functional domains. At eye opening, Nphp5(-/-) mice exhibited absence of scotopic and photopic electroretinogram responses, a phenotype that resembles Leber congenital amaurosis. Outer segment transmembrane protein accumulation in Nphp5(-/-) endoplasmic reticulum was evident as early as postnatal day (P)6. EGFP-CETN2, a centrosome and transition zone marker, identified basal bodies in Nphp5(-/-) photoreceptors, but without fully developed transition zones. Ultrastructure of P6 and 10 Nphp5(-/-) photoreceptors revealed aberrant transition zones of reduced diameter. Nphp5(-/-) photoreceptor degeneration was complete at 1 mo of age but was delayed significantly in Nphp5(-/-);Nrl(-/-) (cone only) retina. Nphp5(-/-) mouse embryonic fibroblast developed normal cilia, and Nphp5(-/-) kidney histology at 1 yr of age showed no significant pathology. Results establish that nephrocystin-5 is essential for photoreceptor outer segment formation but is dispensable for kidney and mouse embryonic fibroblast ciliary formation.
KW  - Senior-LOken syndrome
KW  - nephronophthisis
KW  - Leber congenital amaurosis
KW  - nephrocystins
Y1  - 2016
U6  - https://doi.org/10.1096/fj.201600511R
SN  - 0892-6638
SN  - 1530-6860
VL  - 30
SP  - 3400
EP  - 3412
PB  - Federation of American Societies for Experimental Biology
CY  - Bethesda
ER  - 
TY  - JOUR
A1  - Sas, Claudia
A1  - Mueller, Frank
A1  - Kappel, Christian
A1  - Kent, Tyler V.
A1  - Wright, Stephen I.
A1  - Hilker, Monika
A1  - Lenhard, Michael
T1  - Repeated Inactivation of the First Committed Enzyme Underlies the Loss of Benzaldehyde Emission after the Selfing Transition in Capsella
JF  - Current biology
N2  - The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [14-17]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella. While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella. We identify the Capsella CNL1 gene encoding cinnamate: CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [18], this identifies cinnamate: CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization.
Y1  - 2016
U6  - https://doi.org/10.1016/j.cub.2016.10.026
SN  - 0960-9822
SN  - 1879-0445
VL  - 26
SP  - 3313
EP  - 3319
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Mehner, T.
A1  - Attermeyer, Katrin
A1  - Brauns, Mario
A1  - Brothers, Soren M.
A1  - Diekmann, J.
A1  - Gaedke, Ursula
A1  - Grossart, Hans-Peter
A1  - Koehler, J.
A1  - Lischke, Betty
A1  - Meyer, N.
A1  - Scharnweber, Inga Kristin
A1  - Syvaranta, J.
A1  - Vanni, M. J.
A1  - Hilt, S.
T1  - Weak Response of Animal Allochthony and Production to Enhanced Supply of
Terrestrial Leaf Litter in Nutrient-Rich Lakes
JF  - Ecosystems
N2  - Ecosystems are generally linked via fluxes of nutrients and energy across their boundaries. For example, freshwater ecosystems in temperate regions may receive significant inputs of terrestrially derived carbon via autumnal leaf litter. This terrestrial particulate organic carbon (POC) is hypothesized to subsidize animal production in lakes, but direct evidence is still lacking. We divided two small eutrophic lakes each into two sections and added isotopically distinct maize litter to the treatment sections to simulate increased terrestrial POC inputs via leaf litter in autumn. We quantified the reliance of aquatic consumers on terrestrial resources (allochthony) in the year subsequent to POC additions by applying mixing models of stable isotopes. We also estimated lake-wide carbon (C) balances to calculate the C flow to the production of the major aquatic consumer groups: benthic macroinvertebrates, crustacean zooplankton, and fish. The sum of secondary production of crustaceans and benthic macroinvertebrates supported by terrestrial POC was higher in the treatment sections of both lakes. In contrast, total secondary and tertiary production (supported by both autochthonous and allochthonous C) was higher in the reference than in the treatment sections of both lakes. Average aquatic consumer allochthony per lake section was 27-40%, although terrestrial POC contributed less than about 10% to total organic C supply to the lakes. The production of aquatic consumers incorporated less than 5% of the total organic C supply in both lakes, indicating a low ecological efficiency. We suggest that the consumption of terrestrial POC by aquatic consumers facilitates a strong coupling with the terrestrial environment. However, the high autochthonous production and the large pool of autochthonous detritus in these nutrient-rich lakes make terrestrial POC quantitatively unimportant for the C flows within food webs.
KW  - stable isotopes
KW  - terrestrial subsidy
KW  - carbon budget
KW  - ecological efficiency
KW  - benthic food web
KW  - pelagic food web
Y1  - 2016
U6  - https://doi.org/10.1007/s10021-015-9933-2
SN  - 1432-9840
SN  - 1435-0629
VL  - 19
SP  - 311
EP  - 325
PB  - Springer
CY  - New York
ER  -