Van Den Boom Research Articles

Three new species in the lichen genus Piccolia (Biatorellaceae, lichenized Ascomycota) from the Palaeotropics

Piccolia A.Massal. is a very small genus of crustose lichens with only six species currently accepted. It is characterized by multispored asci, a chlorococcoid photobiont and the presence of anthraquinone pigments in the apothecia (Hafellner 1995, Smith et al. 2009). Hafellner (1995) removed the genus Piccolia A.Massal. from synonymy with Biatorella De Not., recognizing four species. Recently Knudsen & Lendemer (2007) transferred B. nannaria (Tuck.) Zahlbr. to P. nan­ naria (Tuck.) Lendemer & Beeching and Hafellner (2004) transferred Strangospora ochrophora (Nyl.) R.A.Anderson to P. ochrophora (Nyl.) Hafellner. No molecular data are available so far, so that the taxonomic position of the genus is uncertain. The current version of Myconet includes Pic­ colia as a genus incertae sedis within the Lecanoromycetes (Lumbsch & Huhndorf 2010). Four of the species, P. elmeri (Vain.) Hafellner, P. hae­ matina (Mull. Arg.) Hafellner, P. nannaria (Tuck.) Lendemer & Beeching and P. wrightii (Tuck.) Hafellner, are restricted to tropical and subtropical regions. The widely distributed P. conspersa (Fee) Hafellner reaches also warm temperate regions and P. ochrophora (Nyl.) Hafellner occurs throughout Europe as well as in North and South America (Hafellner 1995, 2004, Knudsen & Lendemer 2007). During a collection trip in D.R.Congo in 2009, one of us (D.E.) discovered a crustose lichen with conspicuous apothecia. Microscopical investigation yielded multispored asci, a chlorococcoid photobiont and the presence in the epihymenium of an orange substance that reacted K+ purplish. During a new expedition in 2012 (COBIMFO project) a second specimen was discovered by the first author. A comparison with herbarium specimens of P. elmeri led us to consider the specimens from Reunion Island (van den Boom et al. 2011) to represent an additional new species. The third species, P. nivea, was found on the Solomon Islands and send to us by the second author.

'The famous and new Italian taste': The Dissemination of Italian Sacred Music in the Southern Netherlands, 1675-1755

The seventeenth- and eighteenth-century diaspora of Italian music and musicians in Europe has been widely investigated, yet only fragmentary attention has been paid to the dissemination of Italian sacred music in the Southern Netherlands. By combining data from music inventories made between 1675 and 1755 and the remains of historical music collections, the present article constitutes a systematic inquiry into the circulation of Italian sacred music within this region. Questions are raised about the repertory that may have been available at a typical church, the proportion of Italian music within ecclesiastical music collections, and the extent to which the sacred repertory was renewed. The channels through which Italian sacred music circulated are mapped, with attention paid to the role of the local music presses, the mobility of musicians, and private donations to churches. Finally, closer consideration of the differences in character between the collections at different institutions clarifies the evolving availability of Italian sacred music within the southern Netherlands and demonstrates how extensive personal music collections, such as those of Vanden Boom and van den Branden de Reeth, influenced the repertories of local churches.

Sixty-Two Species of Lirelliform Graphidaceae (Ascomycota) New to Panama, Including Four Species New to Science

VAN DEN BOOM, P. P. G. & SIPMAN, H. J. M. 2013. Sixty-two species of lirelliform Graphidaceae (Ascomycota) new to Panama, including four species new to science. — Herzogia 26: 9–20.Based on fieldwork in 2010 and literature study, 71 species of Graphidaceae s. str. are reported from Panama. Sixtytwo species are new to the country including three species previously known only from their types: Graphis cupei, G. pseudoserpens and G. subflexibilis. Four species are newly described: Acanthothecis salazinica, A. maritima, Graphis fissurinoides and Phaeographis boquetensis.

Abstract 1211: High throughput somatic mutation profiling in non-small cell lung adenocarcinoma using MALDI-TOF Mass spectrometry.

Abstract In the current era of genomics, lung cancer research has made great strides in dissecting the molecular basis of individual tumors. As more mutations are identified, it is clear that the research community needs to interrogate multiple genes to generate an accurate molecular profile for each individual tumor. Molecular classification of large sample sets requires a flexible high-throughput solution that can easily adapt to newly discovered mutations as well as detect minority alleles of mutated DNA. Validation of key mutations requires screening against thousands of samples with a more directed, high-throughput technique such as MALDI-TOF mass spectrometry (MassARRAY® system). We have evaluated the LungCarta™ Panel, a panel targeting 213 somatic mutations in 26 genes frequently mutated in Non-Small Cell Lung Adenocarcinoma (NSCLC). The method relies on multiplex PCR followed by single base extension and analysis using MALDI-TOF Mass Spectrometry. This panel was designed from a candidate pool of more than 1000 mutations identified in the large scale sequencing study with further selection and priority given to mutations that may be implicated in key pathways or of interest for clinical research. Frequently mutated genes such as EGFR, KRAS, BRAF and NRAS are well-represented and newly identified genes were included for further confirmation against larger sample numbers including MAP2K1, EPHA3, NTRKs, STK11, TP53 and DDR2. For verification of this panel we have screened a set of 37 lung tumor DNA samples isolated from formalin fixed paraffin embedded (FFPE) NSCL Adenocarcinomas. These samples were previously characterized for EGFR, KRAS, ERBB2, PIK3CA and BRAF. We identified mutations in 23 samples (62%) localized in 10 genes including 9 novel mutations and all of the 13 previously known mutations were verified. Interestingly, four of the samples contained more than one mutation with two samples carrying 2 separate mutations in the EGFR gene. In addition, by performing a quality test of the FFPE DNA we were able to significantly reduce the DNA amount used for testing, a necessity as the amount of DNA obtained from NSCLC FFPE sample is low. In conclusion, we show that MALDI-TOF mass spectrometry is an ideal tool for high-throughput screening of these types of genetic lesions in NSCLC. The LungCarta Panel provides a targeted, mid-density research panel for cost-effective and rapid analysis. Key somatic mutations in previously annotated genes and pathways can be rapidly confirmed against larger sample numbers. The discovery and confirmation of mutation profiles by tumor subtype will supplement other clinical research observations such as histology and grade to uncover new directions in translational and clinical research on NSCLC. Citation Format: Antoinette Lemoine, Raphael Saffroy, Nelly Bosselut, Jean-Francois Morere, Aleksey Nakorchevsky, Dirk van den Boom, Mathias Ehrich, Darryl Irwin, Anders Nygren. High throughput somatic mutation profiling in non-small cell lung adenocarcinoma using MALDI-TOF Mass spectrometry. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1211. doi:10.1158/1538-7445.AM2013-1211

Plectocarpon dirinariae (Arthoniales), a new lichenicolous species from Cape Verde

AbstractPlectocarpon dirinariae Ertz & van den Boom is described from Cape Verde from the thallus of saxicolous Dirinariaapplanata. The new species is characterized by convex rounded ascomata not inducing basally constricted galls, non-carbonized sterile stromatic tissue, mainly 4–6-spored asci and 3-septate ascospores. Similar Plectocarpon sp. are discussed.

Discovering the Lichen Diversity of a Remote Tropical Island: Working List of Species Collected on Reunion (Mascarene Archipelago, Indian Ocean)

van den Boom, P. P. G., Brand, M., Ertz, D., Kalb, K., Magain, N., Masson, D., Schiefelbein, U., Sipman, H. J. M. & Sérusiaux, E. 2011. Discovering the lichen diversity of a remote tropical island: working list of species collected on Reunion (Mascarene archipelago, Indian Ocean). — Herzogia 24: 325–349.463 lichen taxa are reported from the island of Reunion (Mascarene archipelago) in the Indian Ocean. This report is based on extensive collections recently made by the authors or hosted in B and LG. A total of c. 600 species is estimated for the number of lichenized fungi present on the island; although this is a low figure for a varied tropical area, this is plausible due to its small size and remoteness. The significance of the lichen diversity of the island lays in its endemics, which need further study for a reliable assessment, and in the occurrence of a poorly known southern hemisphere element (“austral” species). The discovery of the following in Reunion is of special interest as it considerably enlarges their distribution range: Anzia corallophora, Caloplaca caesiosorediata, Coccocarpia delicatula, Fuscopannaria praetermissa, Gomphillus morchelloides, G. pedersenii, Gyalideopsis bispora, Heterodermia koyana, Hypotrachyna evansii, Lithogyalideopsis zeylandica, Lobaria asperula, Megaloblastenia marginiflexa var. dimota, Menegazzia capitata, Myeloconis erumpens and Pannaria squamulosa.

Functional and Metabolic Effects of Adaptive Glycerol Kinase (GLPK) Mutants in Escherichia coli

Herein we measure the effect of four adaptive non-synonymous mutations to the glycerol kinase (glpK) gene on catalytic function and regulation, to identify changes that correlate to increased fitness in glycerol media. The mutations significantly reduce affinity for the allosteric inhibitor fructose-1,6-bisphosphate (FBP) and formation of the tetramer, which are structurally related, in a manner that correlates inversely with imparted fitness during growth on glycerol, which strongly suggests that these enzymatic parameters drive growth improvement. Counterintuitively, the glpK mutations also increase glycerol-induced auto-catabolite repression that reduces glpK transcription in a manner that correlates to fitness. This suggests that increased specific GlpK activity is attenuated by negative feedback on glpK expression via catabolite repression, possibly to prevent methylglyoxal toxicity. We additionally report that glpK mutations were fixed in 47 of 50 independent glycerol-adapted lineages. By far the most frequently mutated locus (nucleotide 218) was mutated in 20 lineages, strongly suggesting this position has an elevated mutation rate. This study demonstrates that fitness correlations can be used to interrogate adaptive processes at the protein level and to identify the regulatory constraints underlying selection and improved growth.

Dual Roles of the Cardin-Weintraub Motif in Multimeric Sonic Hedgehog

The fly morphogen Hedgehog (Hh) and its mammalian orthologs, Sonic, Indian, and Desert hedgehog, are secreted signaling molecules that mediate tissue patterning during embryogenesis and function in tissue homeostasis and regeneration in the adult. The function of all Hh family members is regulated at the levels of morphogen multimerization on the surface of producing cells, multimer release, multimer diffusion to target cells, and signal reception. These mechanisms are all known to depend on interactions of positively charged Hh amino acids (the Cardin-Weintraub (CW) motif) with negatively charged heparan sulfate (HS) glycosaminoglycan chains. However, a precise mechanistic understanding of these interactions is still lacking. In this work, we characterized ionic HS interactions of multimeric Sonic hedgehog (called ShhNp) as well as mutant forms lacking one or more CW residues. We found that deletion of all five CW residues as well as site-directed mutagenesis of CW residues Lys(33), Arg(35), and Lys(39) (mouse nomenclature) abolished HS binding. In contrast, CW residues Arg(34) and Lys(38) did not contribute to HS binding. Analysis and validation of Shh crystal lattice contacts provided an explanation for this finding. We demonstrate that CW residues Arg(34) and Lys(38) make contact with an acidic groove on the adjacent molecule in the multimer, suggesting a new function of these residues in ShhNp multimerization rather than HS binding. Therefore, the recombinant monomeric morphogen (called ShhN) differs in CW-dependent HS binding and biological activity from physiologically relevant ShhNp multimers, providing new explanations for functional differences observed between ShhN and ShhNp.

Verrucaria breussii, a New Name for Verrucaria sorbinea Breuss

DIEDERICH, P. & VAN DEN BOOM, P. 2011. Verrucaria breussii, a new name for Verrucaria sorbinea Breuss. — Herzogia 24: 145–146. The name Verrucaria sorbinea Breuss is recognized as a later homonym of Verrucaria sorbina Nyl. ex Hulting. As both species are distinct, a new name, Verrucaria breussii Diederich & van den Boom, is proposed here to replace Verrucaria sorbinea Breuss.

Noninvasive prenatal tests for Down syndrome are near

Noninvasive prenatal tests for Down syndrome are near

Molecular Recognition of the Tes LIM2–3 Domains by the Actin-related Protein Arp7A

Actin-related proteins (Arps) are a highly conserved family of proteins that have extensive sequence and structural similarity to actin. All characterized Arps are components of large multimeric complexes associated with chromatin or the cytoskeleton. In addition, the human genome encodes five conserved but largely uncharacterized “orphan” Arps, which appear to be mostly testis-specific. Here we show that Arp7A, which has 43% sequence identity with β-actin, forms a complex with the cytoskeletal proteins Tes and Mena in the subacrosomal layer of round spermatids. The N-terminal 65-residue extension to the actin-like fold of Arp7A interacts directly with Tes. The crystal structure of the 1–65Arp7A·LIM2–3Tes·EVH1Mena complex reveals that residues 28–49 of Arp7A contact the LIM2–3 domains of Tes. Two alanine residues from Arp7A that occupy equivalent apolar pockets in both LIM domains as well as an intervening GPAK linker that binds the LIM2–3 junction are critical for the Arp7A-Tes interaction. Equivalent occupied apolar pockets are also seen in the tandem LIM domain structures of LMO4 and Lhx3 bound to unrelated ligands. Our results indicate that apolar pocket interactions are a common feature of tandem LIM domain interactions, but ligand specificity is principally determined by the linker sequence.

Structure and Dynamics of the First Archaeal Parvulin Reveal a New Functionally Important Loop in Parvulin-type Prolyl Isomerases

Parvulins are a group of peptidyl-prolyl isomerases (PPIases) responsible for important biological processes in all kingdoms of life. The PinA protein from the psychrophilic archaeon Cenarchaeum symbiosum is a parvulin-like PPIase. Due to its striking similarity to the human parvulins Pin1 and Par14, PinA constitutes an interesting subject for structural and functional studies. Here, we present the first high resolution NMR structure of an archaeal parvulin, PinA, based on 1798 conformational restraints. Structure calculation yields an ensemble of 20 convergent low energy structures with a backbone r.m.s.d. value of 0.6 Å within the secondary structure elements. The overall fold of PinA comprises the β-α3-β-α-β2 fold typical for all parvulin structures known so far, but with helix III being a short 310-helix. A detailed comparison of this high resolution structure of the first archaeal PinA protein with bacterial and eukaryotic parvulin PPIase structures reveals an atypically large catalytic binding site. This feature provides an explanation for cold-adapted protein function. Moreover, the residues in and around 310-helix III exhibit strong intramolecular dynamics on a microsecond to millisecond timescale and display structural heterogeneity within the NMR ensemble. A putative peptide ligand was found for PinA by phage display and was used for 1H-15N-HSQC titrations. Again, the flexible region around 310-helix III as well as residues of the peptide binding pocket showed the strongest chemical shift perturbations upon peptide binding. The local flexibility of this region also was modulated by ligand binding. A glycine and two positively charged residues are conserved in most parvulin proteins in this flexible loop region, which may be of general functional importance for parvulin-type PPIases.

Rinodina etayoi, anew saxicolous lichen species from the Canary Islands

AbstractThe silicicolous lichen species,Rinodina etayoiGiralt & van den Boom, is described as new from inland localities of Fuerteventura and Lanzarote (Canary Islands). It is characterized by a crustose, whitish thallus containing atranorin, zeorin, chloroatranorin and stictic acid, hemispheric pseudolecanorine apothecia containing, a proper exciple inspersed with numerous and large oil drops, and by ascospores of theMischoblastia-type. The joint occurrence of pannarin, stictic acid andMischoblastia-type ascospores makesR. etayoiunique within the genus.

NewRinodinaspecies from the Cape Verde Islands, with notes on some additional species

AbstractExamination ofRinodinaspecimens from the Cape Verde Islands revealed three new species, which are described here:Rinodina capeverdeanaGiralt & van den Boom,R. inspersoparietataGiralt & van den Boom andR. polymorphaesporaGiralt & van den Boom. Additional information is given for six further species, of which five are new records for the archipelago.Rinodina punctosorediataAptroot & Sparrius was found to be conspecific withR. sticticaSheard & Tønsberg.

Reduced Spike-Timing Reliability Correlates with the Emergence of Fast Ripples in the Rat Epileptic Hippocampus

Ripples are sharp-wave-associated field oscillations (100-300 Hz) recorded in the hippocampus during behavioral immobility and slow-wave sleep. In epileptic rats and humans, a different and faster oscillation (200-600 Hz), termed fast ripples, has been described. However, the basic mechanisms are unknown. Here, we propose that fast ripples emerge from a disorganized ripple pattern caused by unreliable firing in the epileptic hippocampus. Enhanced synaptic activity is responsible for the irregular bursting of CA3 pyramidal cells due to large membrane potential fluctuations. Lower field interactions and a reduced spike-timing reliability concur with decreased spatial synchronization and the emergence of fast ripples. Reducing synaptically driven membrane potential fluctuations improves both spike-timing reliability and spatial synchronization and restores ripples in the epileptic hippocampus. Conversely, a lower spike-timing reliability, with reduced potassium currents, is associated with ripple shuffling in normal hippocampus. Therefore, fast ripples may reflect a pathological desynchronization of the normal ripple pattern.

Caloplaca awasthii, a new lichen species from India

The warm, dry climate in central India provides suitable conditions for the growth of many crustose lichens, including Caloplaca species. A new species, Caloplaca awasthii Joshi, Y. & Upreti, is described from this region, where it is found growing in rocky areas of Madhya Pradesh (Bedinagar Hills and Bhimbetka) and Rajasthan (Mount Abu). The new taxon belongs to the section Gasparrinia and is characterized by the presence of blastidia, but lacks apothecia and pycnidia. It is a saxicolous species and is similar to C. decipiens (Arnold) Blomb. & Fross., but differs in having blastidia instead of soredia which are present in C. decipiens. Another closely related species, C. fuerteventurae van den Boom & Etayo, belonging to the C. flavescens complex, differs from the new taxon in having numerous apothecia and citriform spores.

Epigenetic Silencing of CYP24 in Tumor-derived Endothelial Cells Contributes to Selective Growth Inhibition by Calcitriol

Calcitriol (1,25-dihydroxycholecalciferol), the most active form of vitamin D, has selective anti-proliferative effects on tumor-derived endothelial cells (TDEC) compared with Matrigel-derived endothelial cells (MDEC). Although both cell types have an intact vitamin D receptor-signaling axis, this study demonstrates that upon treatment with calcitriol, 24-hydroxylase (CYP24) mRNA, protein and enzymatic activity were markedly induced in MDEC in a time-dependent manner but not in TDEC. Furthermore, treatment of MDEC with a CYP24 small interfering RNA restored sensitivity to calcitriol. To investigate the lack of CYP24 induction in TDEC, we examined methylation patterns in the promoter regions of the CYP24 gene in these two cell types. We identified two putative CpG island regions located at the 5' end. Using methylation-specific PCR and bisulfite sequencing, we determined that these CpG islands were hypermethylated in TDEC but not in MDEC. These data may explain the recruitment of vitamin D receptor to the promoter region in MDEC but not TDEC, as revealed by chromatin immunoprecipitation analyses. Treatment of TDEC with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine restored calcitriol-mediated induction of CYP24, which led to loss of sensitivity to calcitriol growth inhibitory effects. CYP24 promoter hypermethylation was also observed in endothelial cells isolated from other tumors but not in endothelial cells isolated from normal mouse tissues. These observations indicate that the methylation status of the CYP24 promoter differs in endothelial cells isolated from different microenvironments (tumor versus normal) and that methylation silencing of CYP24 contributes to selective calcitriol-mediated growth inhibition in endothelial cells.

Editorial Introduction: Analyzing (Self-)Monitoring in Computer Assisted Learning

Recent generations of empirical research have emphasized the role of cognitive (cf. Dijkstra, Krammer, & van Merrienboer, 1992; Lewalter, 2003) as well as metacognitive strategies in computer-assisted learning (Simons & De Jong, 1992; van den Boom, Paas, van Merrienboer, & van Gog, 2004; Veenman, 1993). Especially the ability of self-monitoring has been shown to be a major moderating variable in self-directed learning with technology (e.g., Herrington & Oliver, 1999; Lan, 1996). However, there still is a need in development as well as application of methods to analyze and improve self-monitoring in individual as well as collaborative computer-assisted learning (CAL). Within this special issue, we combine methods from analyzing self-monitoring within individual and collaborative CAL showing foundational similarities as well as diversities in application. Three articles in this special issue contribute to analysis and fostering of individual CAL focusing on metacognition. The article provided by Elmar Stahl, Stephanie Pieschl, and Rainer Bromme addresses the influence of epistemological beliefs on metacognitive calibration during hypermedia learning. The effect of different epistemological instructions and beliefs on metacognitive calibration and learning outcomes is examined. Therefore, authors investigate in their study if learners are able to differentiate between tasks of different complexity, perform task and goal analyzes, and adapt their learning progress behavior to these self-monitoring outcomes. Furthermore, the role of epistemological beliefs on this self-directed, adaptive process is analyzed. Stahl et al. were able to show that there is a significant relationship between task

Caloplaca squamuloisidiata, a new lichen species from Portugal and Spain

Caloplaca squamuloisidiata van den Boom & V. J. Rico is described as new to science. It is a saxicolous species, pale green to grey, with olivaceous patches, with a rimose-areolate, squamulose, lobulate and isidiate thallus, growing on inland exposed acid rock faces in the western half of the Iberian Peninsula in the Mediterranean region. Its ecology and distribution, and the lichen communities in which it was found are presented. A key to the isidiate and granular-isidiate Caloplaca species in Western Europe is also included.

Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes

The ability of biological systems to adapt to genetic and environmental perturbations is a fundamental but poorly understood process at the molecular level. By quantifying metabolic fluxes and global mRNA abundance, we investigated the genetic and metabolic mechanisms that underlie adaptive evolution of four metabolic gene deletion mutants of Escherichia coli (delta pgi, delta ppc, delta pta, and delta tpi) in parallel evolution experiments of each mutant. The initial response to the gene deletions was flux rerouting through local bypass reactions or normally latent pathways. The principal effect of evolution was improved capacity of already active pathways, whereas new flux distributions were not observed. Combinatorial changes in capacity and pathway activation, however, led to different intracellular flux states that enabled evolution in three of the four parallel cases tested. The molecular bases of the evolved phenotypes were then elucidated by global mRNA transcript analyses. Activation of latent pathways and flux changes in the tricarboxylic acid cycle were found to correlate well with molecular changes at the transcriptional level. Flux alterations in other central metabolic pathways, in contrast, were apparently not connected to changes in the transcriptional network. These results give new insight into the dynamics of the evolutionary process by demonstrating the flexibility of the metabolic network of E. coli to compensate for genetic perturbations and the utility of combining multiple high throughput data sets to differentiate between causal and noncausal mechanistic changes.