Ostracod recovery in the aftermath of the Permian–Triassic crisis: Palaeozoic–Mesozoic turnover

Results of a detailed bathymetric survey of Crater Lake conducted in 2000, combined with previous results of submersible and dredge sampling, form the basis for a geologic map of the lake floor and a model for the filling of Crater Lake with water. The most prominent landforms beneath the surface of Crater Lake are andesite volcanoes that were active as the lake was filling with water, following caldera collapse during the climactic eruption of Mount Mazama 7700 cal. yr B.P. The Wizard Island volcano is the largest and probably was active longest, ceasing eruptions when the lake was 80 m lower than present. East of Wizard Island is the central platform volcano and related lava flow fields on the caldera floor. Merriam Cone is a symmetrical andesitic volcano that apparently was constructed subaqueously during the same period as the Wizard Island and central platform volcanoes. The youngest postcaldera volcanic feature is a small rhyodacite dome on the east flank of the Wizard Island edifice that dates from 4800 cal. yr B.P. The bathymetry also yields information on bedrock outcrops and talus/debris slopes of the caldera walls. Gravity flows transport sediment from wall sources to the deep basins of the lake. Several debris-avalanche deposits, containing blocks up to 280 m long, are present on the caldera floor and occur below major embayments in the caldera walls. Geothermal phenomena on the lake floor are bacterial mats, pools of solute-rich warm water, and fossil subaqueous hot spring deposits. Lake level is maintained by a balance between precipitation and inflow versus evaporation and leakage. High-resolution bathymetry reveals a series of up to nine drowned beaches in the upper 30 m of the lake that we propose reflect stillstands subsequent to filling of Crater Lake. A prominent wave-cut platform between 4 m depth and present lake level that commonly is up to 40 m wide suggests that the surface of Crater Lake has been at this elevation for a very long time. Lake level apparently is limited by leakage through a permeable layer in the northeast caldera wall. The deepest drowned beach approximately corresponds to the base of the permeable layer. Among a group of lake filling models, our preferred one is constrained by the drowned beaches, the permeable layer in the caldera wall, and paleoclimatic data. We used a precipitation rate 70% of modern as a limiting case. Satisfactory models require leakage to be proportional to elevation and the best fit model has a linear combination of 45% leakage proportional to elevation and 55% of leakage proportional to elevation above the base of the permeable layer. At modern precipitation rates, the lake would have taken 420 yr to fill, or a maximum of 740 yr if precipitation was 70% of the modern value. The filling model provides a chronology for prehistoric passage zones on postcaldera volcanoes that ceased erupting before the lake was filled.     

Improved efficiency and stability of multiple cloned gene insertions at the δ sequences of Saccharomyces cerevisiae

Two δ-integration vectors were evaluated for the insertion of an inducible expression cassette (the yeast CUP1 promoter fused to the Escherichia coli lacZ structural gene, CUP1p-lacZ) and a bacterial neomycin-resistance gene (neo) into the genome of Saccharomyces cerevisiae via homologous recombination. Cells containing integrations were selected by resistance to the aminoglycoside G418. The first vector was a traditional construct containing only one δ sequence; with this vector, the transformation efficiency and the number of integrations per cell were quite low. The second carried two δ sequences flanking the desired insert, and the unneeded bacterial sequences were removed by restriction-enzyme digestion immediately before transformation. When this double δ vector was employed, the integrated copy number was more than doubled relative to the single δ system and final β-galactosidase levels exceeded those obtained with the 2μ-based plasmid. Furthermore, the integrations appeared more stable in long-term sequential culture (both with and without induction of the lacZ gene) than those obtained via the single δ vector. Received: 2 December 1996 / Received revision: 21 March 1997 / Accepted: 13 April 1997     

Comparing the efficiency of the laccase–NHA and laccase–HBT systems in eucalyptus pulp bleaching

Laccase–mediator systems have the disadvantage that the mediator is expensive and potentially toxic. In this work, we used N-hydroxyacetanilide (NHA) in combination with laccase for the first time to bleach eucalypt pulp and found it to be a very promising, advantageous alternative to 1-hydroxybenzotriazole (HBT) as mediator. Thus, NHA is efficiently oxidized by laccase to a radical that absorbs light at 350 nm. Also, NHA is a better substrate for laccase than is HBT. An innovative result is that the enzyme is inactivated to a similar extent by both mediators under the typical treatment conditions of the bleaching step (L). This adverse effect, however, is strongly reduced in the presence of pulp. Moreover, the laccase–NHA system is as efficient as the laccase–HBT system in reducing the kappa number of eucalyptus pulp. Using a xylanase pretreatment or unbleached pulp boosts kappa number reduction and bleaching with the laccase–mediator system. Based on the results of cyclic voltammetry tests, NHA has a slightly lower redox potential than HBT, which further supports use of the former; also, unlike HBT, NHA is oxidized in a reversible, pH-dependent manner. Interestingly, the laccase–NHA system provides more efficient bleaching of eucalyptus pulp at pH 5 than it does at pH 4.     

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to the formation of a small region of positive electrostatic potential opposite the covalent bond to the halogen, called the ‘sigma hole.’ Empirical force fields in which the electrostatic interactions are represented by atom-centered point charges cannot capture this effect because halogen atoms usually carry a negative charge and therefore interact unfavorably with other electronegative atoms. A strategy to overcome this problem is to attach a positively charged virtual particle to the halogen. In this work, we extend the additive CHARMM General Force Field (CGenFF) to include such interactions in model systems of phenyl-X, with X being Cl, Br or I including di- and trihalogenated species. The charges, Lennard-Jones parameters, and halogen-virtual particle distances were optimized to reproduce the orientation dependence of quantum mechanical interaction energies with water, acetone, and N-methylacetamide as well as experimental pure liquid properties and relative hydration free energies with respect to benzene. The resulting parameters were validated in molecular dynamics simulations on small-molecule crystals and on solvated protein–ligand complexes containing halogenated compounds. The inclusion of positive virtual sites leads to better agreement across experimental observables, including preservation of ligand binding poses as a direct result of the improved representation of halogen bonding.     

Partial recovery of the population of Corncrakes Crex crex in Britain, 1993–2004

Capsule Singing male Corncrakes increased more than two-fold over the study period.

Aim To provide updated counts of the number and distribution of singing male Corncrakes in Britain and describe the implementation of schemes in which land management was modified to benefit Corncrakes.

Methods Annual surveys of singing Corncrakes in the core of the range in Britain were undertaken between 1993 and 2004 and the total population of the species throughout Britain was assessed in 2003. Annual information on the extent and location of the various conservation management schemes was obtained from the authorities that administer them.

Results Following a long-term decline, the count of Corncrakes in the core of the species' British range increased in ten of the 11 years since 1993. A survey of the core of the range in 2004 located 1040 singing males, a 2.3-fold increase on the 446 singing males located in the same area in 1993. A full survey of Britain and the Isle of Man in 2003 located 832 singing males in 81 10-km National Grid squares. This compares with 589 birds in 93 squares in the last full survey in 1998, and 480 birds in 83 squares in 1993. During 1993–2003, more than 70% of Corncrakes in the core area occurred in 1-km National Grid squares in which conservation schemes were implemented. For males in squares with some conservation management, the average area of managed land to which each bird potentially had exclusive access was about 5 hectares. About half of the tall grass present in 1-km squares occupied by Corncrakes was included in schemes intended to modify mowing or grazing to reduce losses of nests and chicks.

Conclusion There has been a partial recovery of the population of Corncrakes in Britain since 1993, reversing a decline that began in the late 19th and early 20th centuries. However, the geographical range of the species, measured as occupied 10-km grid squares, has not increased. The recovery occurred during a period in which a significant area of land, to which the majority of Corncrakes had access, was entered into conservation management schemes intended to benefit the species. Estimated changes in breeding productivity likely to be associated with changes in grass-mowing management on the observed scale were approximately sufficient to account for the observed change in population trend.     

No peptide left behind: the “out of range” recovery in IPG–IEF fractionation

IEF is often used in multidimensional shotgun proteomics and the narrow range of 3.5–4.5 is the recommended pH interval for the fractionation of tryptic peptides. Usually, even if IEF is performed in IPG strip with a narrow range pH, the entire sample must be loaded onto the strip, including the “out of IPG range” peptides. We describe a simple protocol to recover at least a part of these missing peptides and show that this recovery significantly influences the overall fractionation result, increasing the number of the identified proteins and the protein coverage.     

Head and neck cancer in the UK: what is expected of cytopathology?

Objective:  This review highlights the role of cytopathology in cancer management within UK Head and Neck Cancer Networks and informs on the issues raised by recent UK Department of Health documents and other UK professional guidance. UK guidance requires the formal involvement of cytopathologists within multidisciplinary cancer teams, with medical and non-medical cytopathology staff setting up and running rapid access lump clinics, and support for image-guided fine needle aspiration cytology (FNAC) services. UK guidance also makes recommendations for training, resources and quality control. This review also highlights the resource gap between best practice evidence-based guidance for head and neck (HN) cancer services and existing UK provision for cytopathology, as evidenced by lack of availability of experienced staff and adequacy of training and quality control (QC). Finally, it stresses the importance in the UK of the Royal College of Pathologists' guidance, which defines the need for training, the experience needed for new consultants, the requirements for audit and QC. The implications for the additional resources required for HN cancer cytopathology services are discussed. Recent professional guidance specifying the provision of HN cancer services in the UK includes a cytopathology service for cancer networks, such as rapid access FNAC clinics. Although these clinics already operate in some institutions, there are many institutions where they do not and where the provision of cytopathology services would have to be restructured. This would need the support of local cancer networks and their acceptance of the detailed requirements for cytopathology, including resources, training and QC. The standards are not defined locally, as Strategic Health Authorities and Primary Care Trusts have been instructed by the Department of Health to support, invest and implement them.     

Proteromorphosis of Neospathodus (Conodonta) during the Permian–Triassic crisis and recovery

The Permian–Triassic evolution of platform conodonts (Gondolellidae) consists mainly of the development of the carina and the platform. During the sublethal environmental stress conditions subsequent to the Permian–Triassic extinction, the Wuchiapingian–Griesbachian Clarkina lineage is replaced by the primitive looking platform-lacking Dienerian–Aegean Neospathodus kummeli–Kashmirella timorensis lineage. It is assumed that, above Jinogondolella denticulata, end of the Capitanian Jinogondolella lineage, “Neospathodus” arcucristatus, an atavistic blade-like homeomorph that lacks a platform, underlies Protoclarkina crofti, of the base of the anagenetic Clarkina lineage. These primitive-looking forms are derived from their immediate ancestors by retrograde evolution, a phenomenon that has been described as proteromorphosis. Such events suggest that proteromorphosis occurs during periods of crisis, with the sudden reappearance of homeomorphic forms that are atavistic representatives of the clade. The phenomenon is further substantiated by several additional retrogradations that pace the Triassic, a period prone to such events.     

Pheromone-mediated mating disruption of Choristoneura rosaceana: is the most attractive blend really the most effective?

An attractive four-component pheromone blend containing a major component Z11-tetradecenyl acetate, and three minor components, E11-tetradecenyl acetate, Z11-tetradecenyl alcohol, and Z11-tetradecenyl aldehyde was tested as a mating disruptant against western Canadian populations of the obliquebanded leafroller, Choristoneura rosaceana (Harris) (Lepidoptera: Tortricidae), in organic apple orchards in British Columbia. Efficacy of this four-component blend was compared to that of partial pheromone blends containing the major component plus one or two minor components. A trapping experiment confirmed that, Conrel® fibre disruption dispensers containing the four-component blend were more attractive than disruption dispensers containing the two- or three-component partial blends. A small-plot protocol was followed to compare atmospheric treatments with these blends as mating disruptants at a release rate of 10 mg ha–1 h–1 and from 1000 dispensers ha–1. Mechanisms of mating disruption, such as false-trail following and camouflage of pheromone plumes, that may be evoked to a greater degree by an attractive blend, did not appear to augment the effectiveness of mechanisms invoked by the less attractive blends, as the proportion of mating among tethered females was equal in plots treated with these blends and was reduced by 85–90% compared to the nontreated control. When the four-component pheromone blend was tested at different release rates, mating disruption in small plots began to break down at a release rate of 1.3 mg ha–1 h–1 using a dispenser density of 1000 ha–1. Above 1.3 mg ha–1 h–1 there was no dose response in release rates tested and at release rates below this dose the proportion of tethered females mating was the same as in the nontreated control. The four-component pheromone blend was tested against, and found to be no more effective than, the two-component partial blend at the threshold release rate of 1.3 mg ha–1 h–1 when it was released from 1000 or 250 disruption dispensers. Our results suggest that disruption mechanisms evoked by the attractive blend did not enhance the mating disruption effect provided by the simple blend, therefore a two-component blend may be useful in an operational mating disruption program for C. rosaceana.     

Evolution of female multiple mating: A quantitative model of the “sexually selected sperm” hypothesis

Explaining the evolution and maintenance of polyandry remains a key challenge in evolutionary ecology. One appealing explanation is the sexually selected sperm (SSS) hypothesis, which proposes that polyandry evolves due to indirect selection stemming from positive genetic covariance with male fertilization efficiency, and hence with a male's success in postcopulatory competition for paternity. However, the SSS hypothesis relies on verbal analogy with “sexy-son” models explaining coevolution of female preferences for male displays, and explicit models that validate the basic SSS principle are surprisingly lacking. We developed analogous genetically explicit individual-based models describing the SSS and “sexy-son” processes. We show that the analogy between the two is only partly valid, such that the genetic correlation arising between polyandry and fertilization efficiency is generally smaller than that arising between preference and display, resulting in less reliable coevolution. Importantly, indirect selection was too weak to cause polyandry to evolve in the presence of negative direct selection. Negatively biased mutations on fertilization efficiency did not generally rescue runaway evolution of polyandry unless realized fertilization was highly skewed toward a single male, and coevolution was even weaker given random mating order effects on fertilization. Our models suggest that the SSS process is, on its own, unlikely to generally explain the evolution of polyandry.     

Influence of the spacer region between the Shine–Dalgarno box and the start codon for fine-tuning of the translation efficiency in Escherichia coli

Translation efficiency contributes several orders of magnitude difference in the overall yield of exogenous gene expression in bacteria. In diverse bacteria, the translation initiation site, whose sequence is the primary determinant of the translation performance, is comprised of the start codon and the Shine–Dalgarno box located upstream. Here, we have examined how the sequence of a spacer between these main components of the translation initiation site contributes to the yield of synthesized protein. We have created a library of reporter constructs with the randomized spacer region, performed fluorescently activated cell sorting and applied next-generation sequencing analysis (the FlowSeq protocol). As a result, we have identified sequence motifs for the spacer region between the Shine–Dalgarno box and AUG start codon that may modulate the translation efficiency in a 100-fold range.     

Evolution of trophic transmission in parasites: the need to reach a mating place?

Although numerous parasite species have a simple life cycle (SLC) and complete their life cycle in one host, there are other parasite species that exploit several host species successively. From an evolutionary perspective, understanding the mix of adaptive and contingent forces shaping the transition from an ancestral single‐host state to such a complex life cycle (CLC) has proved an intriguing challenge. In this paper, we propose a new hypothesis, which states that CLCs involving trophic transmission (i.e. transmission to a predator) evolved because they are an efficient way for parasites to meet a sexual partner, assuming that selective benefits are associated with cross‐fertilization. Predators that eat a lot of prey in a relatively short time interval act to concentrate isolated parasites. We use an optimality model to develop our hypothesis and discuss further directions of potential research.     

Emulsification efficiency of adsorbed chitosan for bacterial cells accumulation at the oil–water interface

The use of bacterial cell or biocatalyst for industrial synthetic chemistry is on the way of significant growth since the biocatalyst requires low energy input compared to the chemical synthesis and can be considered as a green technology. However, majority of natural bacterial cell surface is hydrophilic which allows poor access to the hydrophobic substrate or product. In this study, Escherichia coli (E. coli) as a representative of hydrophilic bacterial cells were accumulated at the oil–water interface after association with chitosan at a concentration range of 0.75–750 mg/L. After association with negatively charged E coli having a ζ potential of ?19.9 mV, a neutralization of positively charged chitosan occurred as evidenced by an increase in the ζ potential value of the mixtures with increasing chitosan concentration up to +3.5 mV at 750 mg/L chitosan. Both emulsification index and droplet size analysis revealed that chitosan-E. coli system is an excellent emulsion stabilizer to date because the threshold concentration was as low as 7.5 mg/L or 0.00075 % w/v. A dramatic increase in the surface hydrophobicity of the E. coli as evidenced by an increase in contact angle from 19 to 88° with increasing chitosan concentration from 0 to 750 mg/L, respectively, resulted in an increase in the stability of oil-in-water emulsions stabilized by chitosan-E. coli system. The emulsion was highly stable even the emulsification was performed under 20 % salt condition, or temperature ranged between 20 and 50 °C. Emulsification was failed when the oil volume fraction was higher than 0.5, indicating that no phase inversion occurred. The basic investigation presented in this study is a crucial platform for its application in biocatalyst industry and bioremediation of oil spill.     

Nitrogen use efficiency of rice reconsidered: What are the key constraints?

Recent field studies on irrigated rice at the IRRI research farm indicate efficient use of fertilizer-N based on plant uptake of applied N, (estimated by N difference), and utilization of acquired N for increased grain yield. These findings contrast with ¹⁵N uptake in microplot studies which underestimate the actual increase in plant N from added fertiliser. Constraints other than uptake efficiency, however, may govern fertiliser-N efficiency in farmers fields. In a study of 44 farmers' fields in Central Luzon, rice yields ranged from 2.5 to 6.2 t ha^-1 and N uptake from 35 to 95 kg N ha^-1 in plots without fertiliser-N addition. Farmers applied from 35 to 240 kg N ha^-1, but there was no relationship between the N rate used by each farmer and the effective soil N supply. Mean N uptake efficiency from fertiliser by N difference was only 36%. We conclude that improved fertiliser-N efficiency by farmers will require a more information-intensive management strategy that makes N fertiliser inputs better fitted to the seasonal pattern of crop N demand and soil N supply.     

Role of the donor nuclei in cloning efficiency: can the ooplasm reprogram any nucleus?

Cloning efficiency has not been dramatically improved after the first success of somatic cell nuclear transfer (SCNT) in sheep in 1997. The reasons for the low efficiency of SCNT embryos must be attributed to the insufficient reprogramming of the donor nucleus in ooplasm. It has been clarified that the methylation and acetylation status are disordered in SCNT embryos and the gene expression pattern is different and widely varied in SCNT embryos, compared with fertilized embryos. In this paper, we focused on the role of the donor nuclei in cloning efficiency, and discuss whether ooplasm can reprogram any nucleus.     

Building of an immunosensor: how can the composition and structure of the thiol attachment layer affect the immunosensor efficiency?

Immunosensors, based on the immobilization of a model rabbit antibody on mixed self-assembled monolayers and Protein A as a linking agent on gold transducers, were elaborated and characterized at each step by modulated polarization-infrared spectroscopy (PM-IRRAS) and occasionally by atomic force microscopy (AFM) and quartz crystal microbalance (QCM). By testing two different mixed SAMs comprising 11-mercaptoundecanoic acid (MUA), together with either decanethiol (C9CH3) or mercaptohexanol (C6OH), the role of the chemical composition and structure of the antibody attachment layer upon the sensor performance was demonstrated.     

Prediction of marine species distribution from presence–absence acoustic data: comparing the fitting efficiency and the predictive capacity of conventional and novel distribution models

The accurate representation of species distribution derived from sampled data is essential for management purposes and to underpin population modelling. Additionally, the prediction of species distribution for an expanded area, beyond the sampling area can reduce sampling costs. Here, several well-established and recently developed habitat modelling techniques are investigated in order to identify the most suitable approach to use with presence–absence acoustic data. The fitting efficiency of the modelling techniques are initially tested on the training dataset while their predictive capacity is evaluated using a verification set. For the comparison among models, Receiver Operating Characteristics (ROC), Kappa statistics, correlation and confusion matrices are used. Boosted Regression Trees (BRT) and Associative Neural Networks (ASNN), which are both within the machine learning category, outperformed the other modelling approaches tested.     

Impedance of the electrogenic Cl− pump inAcetabularia: Electrical frequency entrainements,voltage-sensitivity,and reaction kinetic interpretation

Summary Reaction kinetic analysis of the electrical properties of the electrogenic Cl^– pump inAcetabularia has been extended from steady-state to nonsteady-state conditions: electrical frequency responses of theAcetabularia membrane have been measured over the range from 1 Hz to 10 kHz at transmembrane potential differences across the plasmalemma (V _m ) between –70 and –240 mV using voltage-clamp techniques. The results are well described by an electrical equivalent circuit with three parallel limbs: a conventional membrane capacitancec _m , a steadystate conductanceg _o (predominantly of the pump pathway plus a minor passive ion conductance) and a conductanceg _s in series with a capacitancec _p which are peculiar to the temporal behavior of the pump. The absolute values and voltage sensitivities of these four elements have been determined:c _m of about 8 mF m^–2 turned out to be voltage insensitive; it is considered to be normal.g _o is voltage sensitive and displays a peak of about 80 S m^–2 around –180 mV. Voltage sensitivity ofg _s could not be documented due to large scatter ofg _s (around 80 S m^–2).c _p behaved voltage sensitive with a notch of about 20 mF m^–2 around –180 mV, a peak of about 40 mF m^–2 at –120 mV and vanishing at –70 mV. When these data are compared with the predictions of nonsteady-state electrical properties of charge transport systems (U.-P. Hansen, J. Tittor, D. Gradmann, 1983,J. Membrane Biol. in press), model A (redistribution of states within the reaction cycle) consistently provides magnitude and voltage sensitivity of the elementsg _o ,g _s andc _p of the equivalent circuit, when known kinetic parameters of the pump are used for the calculations. This analysis results in a density of pump elements in theAcetabularia plasmalemma of about 50 nmol m^–2. The dominating rate constants for the redistribution of the individual states of the pump in the electric field turn out to be in the range of 500 sec^–1, under normal conditions.