Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species—Leptogorgia virgulata and Leptogorgia hebes—from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil‐calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.     

Toward a plant-based proxy for the isotope ratio of atmospheric water vapor

Atmospheric water vapor is a major component of the global hydrological cycle, but the isotopic balance of vapor is largely unknown. Here, using models and observations, we show that the leaf water δ¹⁸O in the tropical Crassulacean acid metabolism (CAM) epiphyte Tillandsia usneoides is controlled by the δ¹⁸O of atmospheric water vapor in a predictable manner, irrespective of precipitation inputs. By taking the leaf‐water‐atmospheric signature as recorded in plant organic material, we have reconstructed the atmospheric water vapor δ¹⁸O signature for Miami, FL, USA between 1878 and 2005 using contemporary and herbarium specimens. T. usneoides ranges from Virginia, USA southwards through the tropics to Argentina, and the CAM epiphytic lifeform is widespread in other species. Therefore, there is significant potential for using epiphytes to reconstruct the isotope ratio of atmospheric water (both δ¹⁸O and δD) for spatial scales that span over 60° of latitude and temporal scales that cover the last century of global temperature increase.     

Morphological recognition of cryptic species in the planktonic foraminifer Orbulina universa

One of the key hypotheses of paleoceanography is that planktonic foraminiferal morphospecies record reasonably stable and homogeneous oceanographic and climatic characteristics over their geographic and stratigraphic ranges. The discovery of numerous genetically-defined cryptic species challenges the morphospecies concept in planktonic foraminifera and paleoceanographic interpretations based on them. Here, we present a combined genetic and biometric analysis of Orbulina universa specimens in the Atlantic, Indian and Pacific Oceans. Our study is based on shells retained after DNA extractions. On those genotyped shells, we perform biometric analyses (shell size and thickness, inner porosity and pore surface distribution). Our genetic data confirm the presence of three cryptic species of O. universa in the world ocean, whose distributions are primarily correlated to the productivity of the surface waters. The Mediterranean species of O. universa is most abundant in the vertically mixed and nutrient-rich areas of the low to mid-latitudes, whereas the Caribbean and Sargasso species occur in stratified and oligotrophic subtropical waters. Our biometric data show no correlation between shell size and inner porosity within each cryptic species of O. universa. Combining Principal Component Analyses with MANOVAs performed on shell pore surface distribution, we demonstrate that the three different cryptic species are characterized by significant morphological differentiation. The Caribbean species typically exhibits large pores and higher porosity values, while the Mediterranean and Sargasso species are characterized by smaller pore areas and shell porosity. A model based upon pore surface distribution correctly assigns 60% to 90% of the specimens to their corresponding genotype. Although the inner shell surface of the Sargasso species resembles that of the Mediterranean species, our model demonstrates that the pore surface distributions of these two cryptic species can be distinguished. Finally, the Sargasso species exhibits significantly thinner shells than the two other cryptic species.     

Ion selectivity of the Kat1 K+ channel pore

Kat1 is a highly selective inward-rectifying K⁺ channel that opens for extended periods under conditions of extreme hyperpolarization. Over 200 point mutants in the pore region of the Kat1 K⁺ channel were generated and examined in the yeast Saccharomyces cerevisiae and Xenopus oocytes to assess the effect of the mutations on ion selectivity. Substitutions at the tyrosine of the signature sequence G-Y-G resulted in the most significant alterations in ion selectivity, consistent with its role in the selectivity filter. However, greater than 80% of the mutations throughout the greater pore region also conferred a defect in selectivity demonstrating that the entire pore of Kat1 contributes to the ion selectivity of this channel. Surprisingly, we identified a novel class of mutant channel that conferred enhanced selectivity of K⁺ over Na⁺. Mutants of this class frequently displayed sensitivity to the competing ion Cs⁺. This finding has led us to speculate that the Kat1 channel pore has evolved to balance not only K⁺/Na⁺ selectivity, but selectivity over Cs⁺, and possibly a wide spectrum of potential competing ions.     

On some commensal Turbellaria of the Canadian East Coast

The brachyurans Chionoecetes opilio and Hyas araneus collected from the east coast of Canada harbour two species of commensal turbellarians. Ectocotyla hirudo (Levinsen) and E. multitesticulata Fleming & Burt are found on the gills and branchial chambers of male and female crabs. The molluscs Crassostrea virginica and Mytilus edulis collected from several locations where they are cultured along the Northumberland strait carry two commensal eulecithophoran turbellarians, both on the gills, viz., Urasloma cyprinae (Graff) and Paravortex gemellipara (Linton), the latter being a new host record. Aspects of the biology and life-history of these turbellarians are discussed, especially in relationship to the biology of their hosts.Abbreviations in the figures A Atrium - An Antrum - C Capsule - CO Common Oviduct - E Embryo - Ep Egg-laying pore - GP Genital Pore - I Intestine - O Ovary - Od Oviduct - Og Ora-genital Pore - Ph Pharynx - Sp Sperm - SV Seminal Vesicle - T Testes - Va Vagina - Y Yolk     

Description of a new epibiotic relationship (Suctorian–Copepoda) in NE Atlantic waters: from morphological to phylogenetic analyses

Paraeuchaeta hebes is one of the most important carnivorous copepods in the coastal upwelling system off Galician waters (Ría de Vigo, NE Atlantic). A suctorian epibiont of the genus Pelagacineta was found attached to the surface of these copepods. The abundance and distribution on the copepod surface were analysed, taking into account the sex of the crustacean, revealing some preference for females and also a different attachment point in both sexes. The morphological study allowed us to identify a new species of this Suctoria epibiont as Pelagacineta hebensis. Moreover, the 18S rRNA gene was partially sequenced to inspect the phylogenetic position of Pelagacineta hebensis within the subclass Phyllopharyngea. The maximum‐likelihood (ML) tree obtained was consistent with the morphological and with previous molecular studies and showed that P. hebensis belongs to the order Endogenina, as a sister clade of the few taxa sequenced within this order. Including new genetic data to the Endogenina will allow building new hypothesis about the evolution of the most derived clade of suctorians.     

Site Selectivity of the Pit Oichnus excavatus Donovan and Jagt Infesting Hemipneustes striatoradiatus (Leske) (Echinoidea) in the Type Maastrichtian (Upper Cretaceous,The Netherlands)

Two tests of the holasteroid echinoid Hemipneustes striatoradiatus (Leske) from the type area of the Maastrichtian Stage (Upper Cretaceous) bear a varied infestation of episkeletozoans (oysters, bryozoan colony, and serpulids), borings (probable Caulostrepsis isp., Oichnus simplex Bromley), surface abrasion (Gnathichnus? isp.), and pits (O. excavatus Donovan and Jagt). Only O. excavatus represents a premortem infestation. In one specimen, the four individual pits of this ichnospecies are each associated with a different ambulacrum and pore pairs that, in life, bore respiratory tube feet; the anterior ambulacrum, of different gross morphology, is not infested. In the second test, three out of four of the same ambulacra are infested, although there are also O. excavatus in the interambulacra. The association between O. excavatus and the ambulacra of the echinoid, and thus its tube feet, is open to several plausible explanations, but most likely provided some form of feeding or protective advantage to the pit-forming organism.     

Colony morphology,age structure,and relative growth of two gorgonian corals,Leptogorgia hebes (Verrill) and Leptogorgia virgulata (Lamarck), from the northerm Gulf of Mexico

Along the northeastern Gulf of Mexico coast, Leptogorgia hebes is the predominant gorgonian at two inner shelf (22 and 27 m) sites, while Leptogorgia virgulata dominates a third shallow (1–2m), inshore site. The axial skeleton of both species is composed of concentric rings which appeared to exhibit annual periodicity. Although age structure of the populations differed between shelf sites, neither colony growth rates, estimated from direct measurements of ring widths plotted on Walford graphs, nor overall branching complexity, determined from bifurcation ratios (R_b), differed between the shelf populations. Larger individuals at the 27m shelf site were simply older than those at the shallower (22m) shelf site. Walford plots of growth increments revealed colony growth of the shallow inshore species to be similar to that of the offshore species.     

Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis)

The Rio Grande cutthroat trout, Oncorhynchus clarkii virginalis, has declined precipitously over the past century, and currently exhibits a highly fragmented distribution within the Canadian, Pecos and Rio Grande river systems of the western United States. The relationships between populations in the three river drainages, and between O. c. virginalis and the closely related taxa O. c. pleuriticus and O. c. stomias, are not well understood. In order to guide management decisions for the subspecies, we investigated the distribution of variation at 12 microsatellite loci and two regions of the mitochondrial genome. We observed a high level of genetic differentiation between O. c. virginalis populations occupying different headwater streams (global F_st = 0.41). However, we found evidence for previous gene flow within the Rio Grande drainage, indicating that inter-population differentiation may have been exacerbated by the recent effects of population fragmentation. Despite large-scale anthropogenic movement of individuals from the Rio Grande into the Canadian and Pecos, the genetic signature of long-term evolutionary independence between the three drainages has been retained.     

Thermocyclops dumonti sp. n. (Crustacea,Copepoda), from a Temporary Waterbody in China

Six species of the genus Thermocyclops have hitherto been known from Chinese freshwaters. A new species is here recorded from a sample collected from an eutrophic pool in central China. It is described and compared using classical morphology and mapping of its pore signature. Thermocyclops dumonti differs from T. kawamurai by absence of ornamentation on prominences of intercoxal plates of P₁‐P₃, by relative length of apical spines of Enp₃P₄ and caudal ramus. It differs from T. dybowskii by ornamentation of P₄ intercoxal plate, relative length of Enp₃P₄ and caudal ramus, by shape of Tmi. As in other species of Thermocyclops, the perforations are bilaterally symmetrical and, species‐specific patterns occur on the cephalosome, metasome, and urosome. Conserved patterns are found elsewhere on the rostrum, cephalosome, metasome, and furcal branches. Based on pore pattern, Thermocyclops dumonti is separated from two close relatives, T. schmeili and T. dybowskii.     

Some observations on the skin ofOxychilus spp. (Fitzinger), with particular reference toO. helveticus (Blum)(Mollusca,Pulmonata, Zonitidae)

Summary A sub-epithelial collagenous layer and pits in the skin have been described inOxychilus spp. The collagen is especially developed beneath the skin on the right side of the body inO. helveticus. It seems to arise from pore cells which previous authors have described in other molluscs. The pits inO. helveticus are lined by cells which together exhibit a gradation of electron densities. This probably represents an accumulation of secretory material and a macroapocrine secretory process has been observed.

---

Zusammenfassung Bei denOxychilus-Arten wurden eine sub-epitheliale Kollagenschicht und Vertiefungen in der Haut beschrieben. Das Kollagen ist besonders ausgebildet unter der HautoberflÄche der rechten Körperseite inO. helveticus. Dies scheint aus den pore cells hervorzugehen, was auch von früheren Autoren in anderen Mollusken beobachtet wurde. Die Vertiefungen inO. helveticus sind umgeben von Zellen, die zusammen eine Abstufung von Elektronendichte zeigen. Wahrscheinlich representiert dies eine Ansammlung von Sekret-Material; ein macroapokriner Sekretionsvorgang wurde beobachtet.

     

The oxygen isotopic signature of soil‐ and plant‐derived sulphate is controlled by fertilizer type and water source

The oxygen isotope signature of sulphate (δ¹⁸O_sulphate) is increasingly used to study nutritional fluxes and sulphur transformation processes in a variety of natural environments. However, mechanisms controlling the δ¹⁸O_sulphate signature in soil–plant systems are largely unknown. The objective of this study was to determine key factors, which affect δ¹⁸O_sulphate values in soil and plants. The impact of an ¹⁸O‐water isotopic gradient and different types of fertilizers was investigated in a soil incubation study and a radish (Raphanus sativus L.) greenhouse growth experiment. Water provided 31–64% of oxygen atoms in soil sulphate formed via mineralization of organic residues (green and chicken manures) while 49% of oxygen atoms were derived from water during oxidation of elemental sulphur. In contrast, δ¹⁸O_sulphate values of synthetic fertilizer were not affected by soil water. Correlations between soil and plant δ¹⁸O_sulphate values were controlled by water δ¹⁸O values and fertilizer treatments. Additionally, plant δ³⁴S data showed that the sulphate isotopic composition of plants is a function of S assimilation. This study documents the potential of using compound‐specific isotope ratio analysis for investigating and tracing fertilization strategies in agricultural and environmental studies.     

Effect of charge,topology and orientation of the electric field on the interaction of peptides with the α‐hemolysin pore

Nanopore analysis is an emerging technique of structural biology which employs nanopores, such as the α‐hemolysin pore, as a biosensor. A voltage applied across a membrane containing a nanopore generates a current, which is partially blocked when a molecule interacts with the pore. The magnitude (I) and the duration (T) of the current blockade provide an event signature for that molecule. Two peptides, CY12(+)T1 and CY12(?)T1 with net charges + 2 and ? 2, respectively, were analysed using different applied voltages and all four possible orientations of the electrodes and pore. The four orientations were vestibule downstream (VD), vestibule upstream (VU), stem downstream (SD) and stem upstream (SU) where vestibule and stem refer to the side of the pore on which the peptide was placed and downstream and upstream refer to the application of a positive or negative electrophoretic force, respectively. For CY12(+)T1, the effect of voltage on the event duration was consistent with translocation in the VD and SD configurations, but only intercalation events were observed in the VU and SU configurations. For CY12(?)T1, translocations were only observed in the VD and VU configurations. The results are interpreted in terms of two energy barriers on either side of the lumen of the pore. The difference in height of the barriers determines the preferred direction of exit. Electroosmotic flow and current rectification due to the pore as well as the dipole moment and charge of the peptide also play significant roles. Thus, factors other than simple electrophoresis are important for determining the interaction of small peptides with the pore. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Observations on the fine structure of Chlamydobotrys stellata,with particular reference to its unusual chloroplast structure

Summary Eight species of Olpidium are reported from freshwater algae and from soils in Iceland. Similarities between Olpidium endogenum and O. entophytum are discussed. On the basis of the specimens at hand and the substrates in which they occur, O. zygnemicola and O. spirogyrae are reduced to synonymy with O. entophytum and O. endogenum respectively. Olpidioid fungi in Oedogonium and sterilized pine pollen are tentatively assigned to the doubtfully distinct species O. saccatum and O. utriculiforme. Olpidium pendulum, O. luxurians, and O. longicollum occur in pine pollen bait in gross water cultures of soil. These three species are only doubtfully distinct entities. Olpidium rhizophlyctidis is reported for the first time from Iceland.     

Nitrogen concentration and δ15N signature of ombrotrophic Sphagnum mosses at different N deposition levels in Europe

Alteration of the global nitrogen (N) cycle because of human‐enhanced N fixation is a major concern particularly for those ecosystems that are nutrient poor by nature. Because Sphagnum‐dominated mires are exclusively fed by wet and dry atmospheric deposition, they are assumed to be very sensitive to increased atmospheric N input. We assessed the consequences of increased atmospheric N deposition on total N concentration, N retention ability, and δ¹⁵N isotopic signature of Sphagnum plants collected in 16 ombrotrophic mires across 11 European countries. The mires spanned a gradient of atmospheric N deposition from about 0.1 up to about 2 g m^?2 yr^?1. Mean N concentration in Sphagnum capitula was about 6 mg g^?1 in less polluted mires and about 13 mg g^?1 in highly N‐polluted mires. The relative difference in N concentration between capitulum and stem decreased with increasing atmospheric N deposition, suggesting a possible metabolic mechanism that reduces excessive N accumulation in the capitulum. Sphagnum plants showed lower rates of N absorption under increasing atmospheric N deposition, indicating N saturation in Sphagnum tissues. The latter probably is related to a shift from N‐limited conditions to limitation by other nutrients. The capacity of the Sphagnum layer to filter atmospheric N deposition decreased exponentially along the depositional gradient resulting in enrichment of the mire pore water with inorganic N forms (i.e., NO₃^?+NH₄⁺). Sphagnum plants had δ¹⁵N signatures ranging from about ?8‰ to about ?3‰. The isotopic signatures were rather related to the ratio of reduced to oxidized N forms in atmospheric deposition than to total amount of atmospheric N deposition, indicating that δ¹⁵N signature of Sphagnum plants can be used as an integrated measure of δ¹⁵N signature of atmospheric precipitation. Indeed, mires located in areas characterized by greater emissions of NH₃ (i.e., mainly affected by agricultural activities) had Sphagnum plants with a lower δ¹⁵N signature compared with mires located in areas dominated by NO_x emissions (i.e., mainly affected by industrial activities).     

Hydrological and biogeochemical controls on the timing and magnitude of nitrous oxide flux across an agricultural landscape

Anticipated increases in precipitation intensity due to climate change may affect hydrological controls on soil N₂O fluxes, resulting in a feedback between climate change and soil greenhouse gas emissions. We evaluated soil hydrologic controls on N₂O emissions during experimental water table fluctuations in large, intact soil columns amended with 100 kg ha^?1 KNO₃‐N. Soil columns were collected from three landscape positions that vary in hydrological and biogeochemical properties (N= 12 columns). We flooded columns from bottom to surface to simulate water table fluctuations that are typical for this site, and expected to increase given future climate change scenarios. After the soil was saturated to the surface, we allowed the columns to drain freely while monitoring volumetric soil water content, matric potential and N₂O emissions over 96 h. Across all landscape positions and replicate soil columns, there was a positive linear relationship between total soil N and the log of cumulative N₂O emissions (r²= 0.47; P= 0.013). Within individual soil columns, N₂O flux was a Gaussian function of water‐filled pore space (WFPS) during drainage (mean r²= 0.90). However, instantaneous maximum N₂O flux rates did not occur at a consistent WFPS, ranging from 63% to 98% WFPS across landscape positions and replicate soil columns. In contrast, instantaneous maximum N₂O flux rates occurred within a narrow range (?1.88 to ?4.48 kPa) of soil matric potential that approximated field capacity. The relatively consistent relationship between maximum N₂O flux rates and matric potential indicates that water filled pore size is an important factor affecting soil N₂O fluxes. These data demonstrate that matric potential is the strongest predictor of the timing of N₂O fluxes across soils that differ in texture, structure and bulk density.     

Diel distribution of copepods across a channel of an overwash mangrove island

The distribution of copepod species and their nauplii was studied in a narrow, blind channel on an overwash mangrove island offshore of Belize. Copepodids were sampled with a pump at five stations across the channel during a diel cycle. Diel changes of copepodid stages II – VI were marked by horizontal dispersal of Dioithona oculata, the dominant species, from swarms in the prop roots along the shore during the day to the edge of the prop root habitat at night. Migration of copepodids back to the prop roots appeared to be controlled endogenously because change from a night to a daytime age structure began before first light. Mean copepodid stage at subsurface depths in the channel and prop root edge decreased from 4.2 (with 6.0 = all adults) to 2.9 at predawn to 1.1 during day. The oceanic Oithona nana and O. simplex, and the coastal zone O. fonsecae were evenly distributed with depth and distance from shore during day and night, with avoidance of prop root shoreline during day. These species were much less abundant than Dioithona oculata in the prop roots, but of comparable or greater abundance in the channel. Coastal zone Acartia spinata exhibited evidence of swarming. Nauplii, sampled with a 25m plankton net, were dominated by harpacticoid (50%) and cyclopoid (34%) nauplii, which generally were more abundant at 1m than at the surface and more abundant at night than the day. Lagrangian current measurements indicated velocities at ebb tide twice those of flood tide (1.9 vs. 0.8 cm s^–1) and a minimal residence time of 5 days, which could result in advection of D. oculata nauplii out of the Lair Channel before their recruitment into swarms as copepodid stage II. Previously reported maximum swimming speeds of swarming D. oculata copepodid stages (2.0 cm s^–1) and greater densities in prop roots and near the benthos may help copepodids avoid advection. The swarming behavior and diel horizontal migration (or dispersal) reported for D. oculata appears analogous to that of limnetic zooplankton, which may swarm among macrophytes along shorelines during the day to avoid visual predators and disperse or migrate away from the shoreline at night.     

SEPTAL PORE STRUCTURE IN TRICHODERMA SATURNISPORUM

Electron microscopic observations of a previously undescribed ascomycetous septal pore structure are presented and discussed. Hyphal septa and septa at the base of phialides in the hyphomycete, Trichoderma saturnisporum Hammill, developed a membrane-bounded, electron-opaque septal pore body which was fine-structurally similar to Woronin bodies. Within a septal pore body, several electron-transparent layers appeared to develop centripetally from the septal pore rim. The number of layers observed varied from two to about five, with lower numbers being more frequently observed. The electron-transparent layers perhaps functioned as a vinculum, binding the septal pore body in place. Questions about the origin and function of septal pore bodies are discussed.     

Alteration of epithelial cell lysosomal integrity induced by bacterial cholesterol‐dependent cytolysins

Bacterial pathogens can interfere during infection with host cell organelles, such as mitochondria, the endoplasmic reticulum‐Golgi system or nuclei. As important cellular functions are often compartmentalized in these organelles, their targeting allows pathogens to manipulate key host functions during infection. Here, we identify lysosomes as a new class of organelles targeted by the pathogenic bacterium Listeria monocytogenes. We demonstrate that extracellular Listeria, via secretion of the pore‐forming toxin listeriolysin O, alters lysosomal integrity in epithelial cells but not in macrophages. Listeriolysin O induces lysosomal membrane permeabilization and release of lysosomal content, such as cathepsins proteases, which remain transiently active in the host cytosol. We furthermore show that other bacterial pore‐forming toxins, such as perfringolysin O and pneumolysin, also induce lysosomes alteration. Together, our data unveil a novel activity of bacterial cholesterol‐dependent cytolysins.     

Adsorption of the polypeptides on a solid surface. III. Behavior of stiff chains in a pore

A strict analytical theory has been developed describing the behavior of a model lattice polymer chain of arbitrary stiffness in a slitlike pore at polymer–adsorbent interaction energies –ε. The thermodynamic characteristics of the system were calculated. It was shown that the transition of the macromolecule from the solution volume inside a pore occurs by the first-order phase transition with evolution of latent heat of adsorption. The transition point –ε = –ε_c is determined by the chain stiffness and is independent of the pore width D. It is shown that in the precritical range, –ε < –ε_c, the free energy ΔF of the macromolecules in the pores is adequately described by the universal dependence ΔF = ΔF(D*/A), where D* is some effective pore width depending on the value of –ε, and A is the length of the Kuhn segment. At high attraction energies, –ε ? –ε_c, the macromolecules are bonded to the pore walls by a great number of units and their free energy depends only on –ε and the chain stiffness, ΔF = ΔF(A, ε). Close to the critical energy –ε ? –ε_c (transition range), ΔF is determined by both the stiffness of the macromolecule and the pore width D: ΔF ～ A²D^?1 for fairly high values of A and D. The possibilities of using porous media as protein stabilizers are discussed, and the value of the stabilizing effect depending on the chain stiffness is estimated.