Force-induced melting of DNA—evidence for peeling and internal melting from force spectra on short synthetic duplex sequences

Overstretching of DNA occurs at about 60–70 pN when a torsionally unconstrained double-stranded DNA molecule is stretched by its ends. During the transition, the contour length increases by up to 70% without complete strand dissociation. Three mechanisms are thought to be involved: force-induced melting into single-stranded DNA where either one or both strands carry the tension, or a B-to-S transition into a longer, still base-paired conformation. We stretch sequence-designed oligonucleotides in an effort to isolate the three processes, focusing on force-induced melting. By introducing site-specific inter-strand cross-links in one or both ends of a 64 bp AT-rich duplex we could repeatedly follow the two melting processes at 5 mM and 1 M monovalent salt. We find that when one end is sealed the AT-rich sequence undergoes peeling exhibiting hysteresis at low and high salt. When both ends are sealed the AT sequence instead undergoes internal melting. Thirdly, the peeling melting is studied in a composite oligonucleotide where the same AT-rich sequence is concatenated to a GC-rich sequence known to undergo a B-to-S transition rather than melting. The construct then first melts in the AT-rich part followed at higher forces by a B-to-S transition in the GC-part, indicating that DNA overstretching modes are additive.     

Molecular phylogeny of Sterrhinae moths (Lepidoptera: Geometridae): towards a global classification

A multigene phylogenetic study was carried out to test current, mostly morphology-based hypotheses on Sterrhinae phylogeny with additional material included from further geographical areas and morphologically different lineages. A maximum likelihood analysis (11 molecular markers and 7665 bp) was conducted on 76 species and 41 genera using iq-tree software. The resulting phylogenetic hypothesis is well resolved and branches have high support values. Results generally agree with earlier hypotheses at tribal levels and support the hypothesis that Sterrhinae comprises two major lineages. Based on the molecular phylogeny and extensive morphological examination, nine tribes are considered valid and the following taxonomic changes are introduced to recognize monophyletic groups: Mecoceratini Guenée, 1858 (= Ametridini Prout, 1910) is transferred from Desmobathrinae to Sterrhinae, and it is considered valid at tribal level new classification ; Haemaleini Sihvonen & Brehm is described as a new tribe and deemed sister to Scopulini + Lissoblemmini; Lissoblemmini Sihvonen & Staude is described as a new tribe and sister to Scopulini; Lythriini Herbulot, 1962 is now a junior synonym of Rhodometrini Agenjo, 1952 syn.n. ; and Rhodostrophiini Prout, 1935 is now a junior synonym of Cyllopodini Kirby, 1892 syn.n. In addition, 48 taxa are transferred from other geometrid subfamilies to Sterrhinae, or within Sterrhinae from one tribe to another, or they are classified into a tribe for the first time, or a new genus classification is proposed. The results demonstrate the limited explanatory power of earlier classifications, particularly at the tribal level. This is probably a result of earlier classifications being based on superficial characters and biased towards the European and North American fauna. The species richness and distribution of Sterrhinae and its constituent tribes are reviewed, showing that the globally distributed Sterrhinae are most diverse in the Neotropics (31% of global fauna). They are species-rich in the Palaearctic (22%), Afrotropics (19%) and Indo-Malay (16%) regions, whereas they are almost absent in Oceania (1%). In terms of the described fauna, the most species-rich tribes are Scopulini (928 species), Sterrhini (876 species) and Cosymbiini (553 species), all of which have a cosmopolitan distribution. Mecoceratiini and Haemaleini are almost entirely Neotropical. Timandrini and Lissoblemmini, by contrast, are absent in the Neotropics. We present a revised classification of the global Sterrhinae fauna, which includes about 3000 putatively valid species, classified into nine tribes and 97 genera. Four genera are of uncertain position within Sterrhinae. Our results highlight the compelling need to include more genera from a global perspective in molecular phylogenetic studies, in order to create a stable global classification for this subfamily. This published work has been registered on ZooBank, http://zoobank.org/urn:lsid:zoobank.org :pub:A66F5DDD-06D6-4908-893E-E8B124BB99B1.     

A phylogenomic tree inferred with an inexpensive PCR-generated probe kit resolves higher-level relationships among Neptis butterflies (Nymphalidae: Limenitidinae)

Recent advances in obtaining reduced representation libraries for next-generation sequencing permit phylogenomic analysis of species-rich, recently diverged taxa. In this study, we performed sequence capture with homemade PCR-generated probes to study diversification among closely related species in a large insect genus to examine the utility of this method. We reconstructed the phylogeny of Neptis Fabricius, a large and poorly studied nymphalid butterfly genus distributed throughout the Old World. We inferred relationships among 108 Neptis samples using 89 loci totaling up to 84 519 bp per specimen. Our taxon sample focused on Palearctic, Oriental and Australasian species, but included 8 African species and outgroups from 5 related genera. Maximum likelihood and Bayesian analyses yielded identical trees with full support for almost all nodes. We confirmed that Neptis is not monophyletic because Lasippa heliodore (Fabricius) and Phaedyma amphion (Linnaeus) are nested within the genus, and we redefine species groups for Neptis found outside of Africa. The statistical support of our results demonstrates that the probe set we employed is useful for inferring phylogenetic relationships among Neptis species and likely has great value for intrageneric phylogenetic reconstruction of Lepidoptera. Based on our results, we revise the following two taxa: Neptis heliodore comb. rev. and Neptis amphion comb. rev.     

Species limits in butterflies (Lepidoptera: Nymphalidae): reconciling classical taxonomy with the multispecies coalescent

Species delimitation is at the core of biological sciences. During the last decade, molecular‐based approaches have advanced the field by providing additional sources of evidence to classical, morphology‐based taxonomy. However, taxonomy has not yet fully embraced molecular species delimitation beyond threshold‐based, single‐gene approaches, and taxonomic knowledge is not commonly integrated into multilocus species delimitation models. Here we aim to bridge empirical data (taxonomic and genetic) with recently developed coalescent‐based species delimitation approaches. We use the multispecies coalescent model as implemented in two Bayesian methods (dissect/stacey and bp&p ) to infer species hypotheses. In both cases, we account for phylogenetic uncertainty (by not using any guide tree) and taxonomic uncertainty (by measuring the impact of using a priori taxonomic assignments to specimens). We focus on an entire Neotropical tribe of butterflies, the Haeterini (Nymphalidae: Satyrinae). We contrast divergent taxonomic opinion – splitting, lumping and misclassifying species – in the light of different phenotypic classifications proposed to date. Our results provide a solid background for the recognition of 22 species. The synergistic approach presented here overcomes limitations in both traditional taxonomy (e.g. by recognizing cryptic species) and molecular‐based methods (e.g. by recognizing structured populations, and not raising them to species). Our framework provides a step forward towards standardization and increasing reproducibility of species delimitations.     

Towards resolving and redefining Amphipyrinae (Lepidoptera,Noctuoidea, Noctuidae): a massively polyphyletic taxon

Amphipyrinae have long been a catchall taxon for Noctuidae, with most members lacking discernible morphological synapomorphies that would allow their assignment to one of the many readily diagnosable noctuid subfamilies. Here data from seven gene regions (> 5500 bp) for more than 120 noctuid genera are used to infer a phylogeny for Amphipyrinae and related subfamilies. Sequence data for 57 amphipyrine genera – most represented by the type species of the genus – are examined. We present here the first large‐scale molecular phylogenetic study of Amphipyrinae and the largest molecular phylogeny of Noctuidae to date; several proposed nomenclatural changes for well‐supported results; and the identification of areas of noctuid phylogeny where greater taxon sampling and/or genomic‐scale data are needed. Adult and larval morphology, along with life‐history traits, for taxonomic groupings most relevant to the results are discussed. Amphipyrinae are significantly redefined; many former amphipyrines, excluded as a result of these analyses, are reassigned to other noctuid subfamily‐level taxa. Four genera, Chamaeclea Grote, Heminocloa Barnes & Benjamin, Hemioslaria Barnes & Benjamin and Thurberiphaga Dyar, are transferred to the tribe Chamaecleini Keegan & Wagner tribe n. in Acontiinae. Stiriina is elevated to Stiriinae rev. stat. , Grotellina is elevated to Grotellinae rev. stat. and Annaphilina is elevated to Annaphilini rev. stat. Acopa Harvey is transferred to Bryophilinae, Aleptina Dyar is transferred to Condicinae, Leucocnemis Hampson and Oxycnemis gracillinea (Grote) are transferred to Oncocnemidinae, Nacopa Barnes & Benjamin is transferred to Noctuinae and Narthecophora Smith is transferred to Stiriinae. Azenia Grote (and its subtribe Azeniina), Cropia Walker, Metaponpneumata Möschler, Sexserrata Barnes & Benjamin and Tristyla Smith are transferred to Noctuidae incertae sedis. Hemigrotella Barnes & McDunnough (formerly in subtribe Grotellina) is retained in Amphipyrinae. Argentostiria Poole and Bistica Dyar are retained in Stiriini but removed from incertae sedis position. This published work has been registered on ZooBank: http://zoobank.org/urn:lsid:zoobank.org:pub:4A140782‐31BA‐445A‐B7BA‐6EAB98ED43FA .     

Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs

The classical Hodgkin-Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied by the resistance of the ion channels, and by the gating time constants. We study slow dynamics in an extended HH framework that includes time-dependent ion concentrations, pumps, and buffers. Fluxes across the neuronal membrane change intra- and extracellular ion concentrations, whereby the latter can also change through contact to reservoirs in the surroundings. Ion gain and loss of the system is identified as a bifurcation parameter whose essential importance was not realized in earlier studies. Our systematic study of the bifurcation structure and thus the phase space structure helps to understand activation and inhibition of a new excitability in ion homeostasis which emerges in such extended models. Also modulatory mechanisms that regulate the spiking rate can be explained by bifurcations. The dynamics on three distinct slow times scales is determined by the cell volume-to-surface-area ratio and the membrane permeability (seconds), the buffer time constants (tens of seconds), and the slower backward buffering (minutes to hours). The modulatory dynamics and the newly emerging excitable dynamics corresponds to pathological conditions observed in epileptiform burst activity, and spreading depression in migraine aura and stroke, respectively.     

Gender Differences in Emotional Responses to Cooperative and Competitive Game Play

Previous research indicates that males prefer competition over cooperation, and it is sometimes suggested that females show the opposite behavioral preference. In the present article, we investigate the emotions behind the preferences: Do males exhibit more positive emotions during competitive than cooperative activities, and do females show the opposite pattern? We conducted two experiments where we assessed the emotional responses of same-gender dyads (in total 130 participants, 50 female) during intrinsically motivating competitive and cooperative digital game play using facial electromyography (EMG), skin conductance, heart rate measures, and self-reported emotional experiences. We found higher positive emotional responses (as indexed by both physiological measures and self-reports) during competitive than cooperative play for males, but no differences for females. In addition, we found no differences in negative emotions, and heart rate, skin conductance, and self-reports yielded contradictory evidence for arousal. These results support the hypothesis that males not only prefer competitive over cooperative play, but they also exhibit more positive emotional responses during them. In contrast, the results suggest that the emotional experiences of females do not differ between cooperation and competition, which implies that less competitiveness does not mean more cooperativeness. Our results pertain to intrinsically motivated game play, but might be relevant also for other kinds of activities.     

Passive elastic wall stiffness of the left ventricle: A comparison between linear theory and large deformation theory

Assuming a spherical geometry for the left ventricle, passive elastic stiffness-stress relations have been obtained on the basis of linear elasticity theory and large deformation theory. Employing pressure-volume aata taken from rat hearts of various age groups, it is shown that young rat heart muscle (1 month) is stiffer than either adult (7 months) or old rat heart muscle (17 months). Although the qualitative results are similar for both elasticity theories, the large deformation theory gave results in closer agreement with those obtained from papillary muscle studies. These results imply that stiffness of muscleper se can be assessed from left ventricular pressure-volume data.     

Chemotaxonomy of Prototaxites and evidence for possible terrestrial adaptation

Silicified and carbonized axes of Prototaxites are chemically analyzed by means of X-ray and organic-extraction techniques. The isolation and identification of cutin and suberin derivatives, i.e., ω-hydroxymonocarboxylic acids, suggest that Prototaxites may have been a terrestrial plant or an aquatic plant showing chemical adaptation to periods of desiccation. Normal saturated acids showing no odd or even carbon-number predominance, phenyl and naphthyl aromatic acids, and normal and aromatic dicarboxylic acids isolated from fossil material, are considered inconsistent with an algal biochemistry. The normal saturated fatty acids isolated from Parka, Pachytheca, Spongiophyton, Protosalvinia, Orestovia and Taeniocrada are compared with Prototaxites. Parka, Pachytheca, Spongiophyton and Orestovia, parallel one another in their organic chemical constituents, while Protosalvinia, Taeniocrada and Prototaxites appear to have paralleled one another in their adaptation to a terrestrial habit.