Genomic Resources Notes accepted 1 October 2013 – 30 November 2013

This article documents the public availability of (i) genomic sequence data and 43 microsatellite loci for the bat species, Lasiurus borealis and Lasiurus cinereus, and (ii) complete mitochondrial and partial nuclear genomes for two jack species, Caranx ignobilis, Caranx melampygus.     

Referees 2013

From August to September 2013, c. 21 specimens of the blue runner Caranx crysos were caught by commercial fishermen in two locations off the south coast of Newfoundland, Canada. These samples represent the first records of C. crysos in Newfoundland waters, and a potential northward range expansion of this species in the north‐western Atlantic Ocean. They also illustrate the importance of fisher‐derived sampling that spans times and locations outside of the limited range targeted by scientific surveys in this region.     

–SH and S–S involvement in Chlamydomonas mating

Reagents that block or cross-link sulfhydryl (–SH) groups and those that reduce disulfide (S–S) bonds have been tested for their effects on mating in Chlamydomonas reinhardii. Wild-type (wt) gametes of mating type + (mt⁺) and mt^?, and a fusion-defective mt^? mutant, gam-11, were studied. Differential sensitivities of mt⁺ vs mt^? and of wt mt^? vs gam-11 mt^? were analyzed. Concentrations of reagents that did not disrupt flagellar agglutination, the first stage of the mating reaction, were generally used. Pretreatment of mt⁺ gametes with the membrane permeable –SH reducing agent dithiothreitol (DTT) inhibits flagellar sexual signaling at concentrations that do not inhibit any part of the mating reaction of mt^? gametes. Wt mt^? is more sensitive than wt mt⁺ to inhibition by low concentrations of p-chloromercuribenzoate sulfonate (pCMBS), an organic mercurial. The membrane-impermeable reducing agent, reduced glutathione (GSH), also preferentially inhibits wt mt^?. Gam-11 mt^?, a fusion-defective mutant, which has been used to study the sensitivity of the adhesion of the plasma membrane-associated mating structures, is less sensitive to GSH and pCMBS inhibition that is wt mt^?. DDT and pCMBS cause an increase in mating structure adhesion in pretreated gam-11. The differential inhibition of pair and group formation during gam-11 × wt mt⁺ matings has suggested a possible mechanism for mating structure adhesion.     

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013–31 March 2013

This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross‐tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii.     

Conformation of amylose–iodine–iodide complex in aqueous solution

The conformational characteristics of the amylose–iodine–iodide complex in aqueous solution, particularly for a rapidly mixed system, were studied by resonance polarized scattering measurements using a He-Ne laser at low concentrations of the complex and by viscosity measurements at high concentrations of the complex. For the scattering measurements, the following results were obtained: the depolarization ratios ρ_u and ρ_v showed a pronounced increase with the degree of saturation of the bound iodine (q) in amylose, depending on KI concentration. At q ? 0.7, the increase in these values appeared to be suppressed. However, the ρ_h value was approximately 1, irrespective of q. Additionally, the dissymmetry Z decreased appreciably with increasing q. The conformational change of the complex with q was characterized by the changes in the contour and persistence lengths of the chain and in the optical anisotropy of the scattering segments, which were obtained from numerical computations based on the polarized scattering equation for a wormlike-chain model with a restriction by the entropy force of the chain. The viscosity of the complex solution decreased with increasing q; above q ? 0.7 it increased strikingly. The conformational change of the complex with q was characterized by the change in exponent α in the Houwink-Mark-Sakurada equation [η] = KM^α. It was concluded that the iodine-saturated complex has the characteristics of a rod, regardless of the complex concentration.     

SnTox5–Snn5: a novel Stagonospora nodorum effector–wheat gene interaction and its relationship with the SnToxA–Tsn1 and SnTox3–Snn3–B1 interactions

The Stagonospora nodorum–wheat interaction involves multiple pathogen‐produced necrotrophic effectors that interact directly or indirectly with specific host gene products to induce the disease Stagonospora nodorum blotch (SNB). Here, we used a tetraploid wheat mapping population to identify and characterize a sixth effector–host gene interaction in the wheat–S. nodorum system. Initial characterization of the effector SnTox5 indicated that it is a proteinaceous necrotrophic effector that induces necrosis on host lines harbouring the Snn5 sensitivity gene, which was mapped to the long arm of wheat chromosome 4B. On the basis of ultrafiltration, SnTox5 is probably in the size range 10–30 kDa. Analysis of SNB development in the mapping population indicated that the SnTox5–Snn5 interaction explains 37%–63% of the variation, demonstrating that this interaction plays a significant role in disease development. When the SnTox5–Snn5 and SnToxA–Tsn1 interactions occurred together, the level of SNB was increased significantly. Similar to several other interactions in this system, the SnTox5–Snn5 interaction is light dependent, suggesting that multiple interactions may exploit the same pathways to cause disease.     

Helix–coil transition and conformational studies of protamine–DNA complexes

Protamine–DNA complexes prepared by the method of direct and slow mixing in 2.5 × 10^?4M EDTA, pH 8.0, have been studied by thermal denaturation and circular dichroism. The complexes show biphasic melting with T_m at about 50 °C corresponding to the melting of free DNA regions and T_m′ at about 92 °C corresponding to the melting of protamine-bound regions. In protamine-bound regions there are 1.38 amino acid residues per nucleotide, indicating a nearly completely charge neutralization. T_m is increased but T_m′ is not when the ionic strength of the buffer is raised. This also supports a full charge neutralization in protamine-bound regions. The circular dichroism of the complexes can be decomposed into two components, Δ_ε0 of free DNA regions in B-form conformation and Δ_εb of protamine-bound regions in a characteristic conformation neither that of B- nor C-form but somewhere between them.     

Electric dichroism studies on ferriheme– and ferroheme–poly(L-lysine) complexes at pH 9–12

Transient electric dichroism has been measured for the ferriheme–poly(L -lysine)[(Lys)_n], ferroheme–(Lys)_n, and ferroheme–(Lys)_n–carbon monoxide (CO) solutions at pH 9–12. The Soret absorption maximum in electronic spectrum (λ), the reduced linear dichroism (ρ_∞) at complete orientation and the calculated angle (?) between the porphyrin plane of a bound heme and the oriented polymer axis are determined for the following complexes: a ferriheme–(Lys)_n complex at pH 9.5–10.5 (λ = 420 nm, ρ_∞ = 0.50, and ? = 19°), a ferroheme–(Lys)_n complex at pH 9.5–10.2 (λ = 432 nm, ρ_∞ = 0.77, and ? = 0°), and a ferroheme–(Lys)_n–CO complex at pH 9.25 (λ = 430 nm, ρ_∞ = 0.38, and ? = 24°). Based on the above data, the validity of the structures of heme–(Lys)_n complexes proposed by other investigators is discussed.     

CRS–MIS in Candida glabrata: sphingolipids modulate echinocandin–Fks interaction

Infections with the azole‐refractory yeast Candida glabrata are now commonly treated with the echinocandins caspofungin (CSF) or micafungin (MCF). True resistance (> 32‐fold decreased susceptibility) to these lipopeptide inhibitors of cell wall synthesis is rare and strictly associated with mutations in integral membrane proteins Fks1 or Fks2. In contrast, mutants exhibiting 4‐ to 32‐fold CSF reduced susceptibility (CRS) were readily selected in vitro, and surprisingly demonstrated 4‐ to 32‐fold MCF increased susceptibility (MIS). Sequencing and gene deletion demonstrated that CRS–MIS is Fks‐independent. To explore alternative mechanisms, we initially employed Saccharomyces cerevisiae, and observed that CRS was conferred by multiple mutations (fen1Δ, sur4Δ, cka2Δ and tsc10‐ts) disrupting sphingolipid biosynthesis. Following this lead, C. glabrata fen1Δ and cka2Δ deletants were constructed, and shown to exhibit CRS–MIS. Sphingolipid analysis of CRS–MIS laboratory mutants and clinical isolates demonstrated elevated dihydrosphingosine (DHS) and phytosphingosine (PHS) levels, and consistent with this sequencing revealed fen1, sur4, ifa38 and sur2 mutations. Moreover, exogenous DHS or PHS conferred a CRS–MIS phenotype on wild‐type C. glabrata. Exogenous PHS failed, however, to suppress CRS–MIS in a sur2 mutant blocked in conversion of DHS to PHS, implying that accumulation of these intermediates confers CRS–MIS. We conclude that membrane sphingolipids modulate echinocandin–Fks interaction.     

Genomic Resources Notes accepted 1 April 2013–31 May 2013

This article documents the public availability of approximately 15 000 polymorphic SNP loci for the bighorn sheep Ovis canadensis.     

Loss of the Birt–Hogg–Dubé gene product folliculin induces longevity in a hypoxia‐inducible factor–dependent manner

Signaling through the hypoxia‐inducible factor hif‐1 controls longevity, metabolism, and stress resistance in Caenorhabditis elegans. Hypoxia‐inducible factor (HIF) protein levels are regulated through an evolutionarily conserved ubiquitin ligase complex. Mutations in the VHL gene, encoding a core component of this complex, cause a multitumor syndrome and renal cell carcinoma in humans. In the nematode, deficiency in vhl‐1 promotes longevity mediated through HIF‐1 stabilization. However, this longevity assurance pathway is not yet understood. Here, we identify folliculin (FLCN) as a novel interactor of the hif‐1/vhl‐1 longevity pathway. FLCN mutations cause Birt–Hogg–Dubé syndrome in humans, another tumor syndrome with renal tumorigenesis reminiscent of the VHL disease. Loss of the C. elegans ortholog of FLCN F22D3.2 significantly increased lifespan and enhanced stress resistance in a hif‐1‐dependent manner. F22D3.2, vhl‐1, and hif‐1 control longevity by a mechanism distinct from insulin‐like signaling. Daf‐16 deficiency did not abrogate the increase in lifespan mediated by flcn‐1. These findings define FLCN as a player in HIF‐dependent longevity signaling and connect organismal aging, stress resistance, and regulation of longevity with the formation of renal cell carcinoma.     

Effect of Enhancers on the Pyridopyridazine–Peroxide–HRP Reaction

4-Substituted phenyl boronic acids (e.g., 4-iodo, 4-bromo, 4-phenyl) are effective enhancers of the horseradish peroxidase (Type VIA) catalysed chemiluminescent oxidation of various pyrido[3,4-d]pyridazine-1,4(2H,3H)dione derivatives. The most effective combination was 4-biphenylboronic acid and 8-amino-5-chloro-7- phenylpyrido[3,4-d]- pyridazine-1,4(2H,3H)dione. Generally, the intensity of light emission in the presence of peroxidase was higher with the pyridopyridazines than with sodium luminol. However, the blank light emission was much lower with sodium luminol than with the pyridopyridazines. A synergistic enhancement phenomenon was demonstrated for the combination of a 4-iodophenol and a 4-biphenylboronic acid enhancer with 8-amino-5-chloro-7-phenylpyrido[3,4-d]pyridazine-1,4(2H,3H)dione. The combination of these two enhancers produced a light emission intensity in an assay for 5 fmol of peroxidase that was 25% higher than expected from the sum of the individual light intensities.     

Evidence for plasticity genotypes in a gene–gene–environment interaction: the TRAILS study

The purpose was to study how functional polymorphisms in the brain derived neurotrophic factor gene (BDNF val66met) and the serotonin transporter gene linked promotor region (5‐HTTLPR) interact with childhood adversities in predicting Effortful Control. Effortful Control refers to the ability to regulate behavior in a goal‐directed manner and is an interesting endophenotype for psychopathology because of its heritability and the association of low Effortful Control with both internalizing and externalizing problems. In a longitudinal population‐based study Effortful Control was assessed with the parent version of the Early Adolescent Temperament Questionnaire at age 11. Pregnancy and delivery adversities and childhood events were assessed in a parent interview at age 11. Long‐term difficulties until age 11 were assessed with a parent questionnaire at age 13.5. Blood or buccal cells were collected at age 16 for genotyping the rs6265 and rs25531 SNPs and the 5‐HTTLPR length polymorphism. The study included 1032 complete data sets. Effortful Control was significantly predicted by the interaction between BDNF val66met, 5‐HTTLPR and childhood events. The BDNF val66met val/val–5‐HTTLPR l′/l′ genotype was unaffected by childhood events, while having either at least one BDNF val66met met or 5‐HTTLPR s′ allele (l′/l′‐met‐carrier; l′/s′‐val/val; s′/s′‐val/val) made children sensitive to childhood events. Predictions of Effortful Control by pregnancy and delivery adversities and long‐term difficulties were largely independent of genotype. We concluded that the l′/l′‐met‐carrier, l′/s′‐val/val and the s′/s′‐val/val genotypes showed greatest plasticity while the l′/l′‐val/val genotype was unaffected by childhood events.     

Pothos vietnamensis sp. nov. (Araceae–Pothoideae–Potheae) from Vietnam

Pothos vietnamensis V. D. Nguyen & P. C. Boyce is described and illustrated from northern Vietnam as a new species of the Pothos supergroup, and it is compared with the two most similar species: P. kerrii and P. pilulifer to which P. vietnamensis is comparable by having a very small fertile portion (< 5 mm diameter) on the spadix. Ecology, habitat, population size and conservation status are also discussed.     

Length–weight and length–length relationships for six commercial fishes from southern Korean waters

Presented are the relationships between total length and weight, and between total length and standard length for six commercial fishes collected twice a month from local fish markets in southern Korea between 2005–2006 for Acanthopagrus schlegelii (Bleeker, 1854), Hexagrammos agrammus (Temminck & Schlegel, 1843) and Hexagrammos otakii (Jordan & Starks, 1895), and monthly in 2004 for Dentex tumifrons (Temminck & Schlegel, 1843), Doederleinia berycoides (Hilgendorf, 1879) and Scomberomorus niphonius (Cuvier, 1832). The LWR for D. tumifrons is estimated for the first time, and a new maximum length was recorded for S. niphonius. All total length and weight relationships were significant (all r² > .953). The values of exponent b, estimated using simple linear least squares of log‐transformed weight and length data, ranged from 2.945 to 3.317.     

Caribbean massive corals not recovering from repeated thermal stress events during 2005–2013

Massive coral bleaching events associated with high sea surface temperatures are forecast to become more frequent and severe in the future due to climate change. Monitoring colony recovery from bleaching disturbances over multiyear time frames is important for improving predictions of future coral community changes. However, there are currently few multiyear studies describing long‐term outcomes for coral colonies following acute bleaching events. We recorded colony pigmentation and size for bleached and unbleached groups of co‐located conspecifics of three major reef‐building scleractinian corals (Orbicella franksi, Siderastrea siderea, and Stephanocoenia michelini; n = 198 total) in Bocas del Toro, Panama, during the major 2005 bleaching event and then monitored pigmentation status and changes live tissue colony size for 8 years (2005–2013). Corals that were bleached in 2005 demonstrated markedly different response trajectories compared to unbleached colony groups, with extensive live tissue loss for bleached corals of all species following bleaching, with mean live tissue losses per colony 9 months postbleaching of 26.2% (±5.4 SE) for O. franksi, 35.7% (±4.7 SE) for S. michelini, and 11.2% (±3.9 SE) for S. siderea. Two species, O. franksi and S. michelini, later recovered to net positive growth, which continued until a second thermal stress event in 2010. Following this event, all species again lost tissue, with previously unbleached colony species groups experiencing greater declines than conspecific sample groups, which were previously bleached, indicating a possible positive acclimative response. However, despite this beneficial effect for previously bleached corals, all groups experienced substantial net tissue loss between 2005 and 2013, indicating that many important Caribbean reef‐building corals will likely suffer continued tissue loss and may be unable to maintain current benthic coverage when faced with future thermal stress forecast for the region, even with potential benefits from bleaching‐related acclimation.