Changes in seasonal climate outpace compensatory density‐dependence in eastern brook trout

Understanding how multiple extrinsic (density‐independent) factors and intrinsic (density‐dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density‐dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) vs. density‐dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10‐year capture‐mark‐recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete‐time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type, and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density‐dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate‐driven environmental change.     

Control Growth Factor Release Using a Self-Assembled [polycation∶heparin] Complex

The importance of growth factors has been recognized for over five decades; however their utilization in medicine has yet to be fully realized. This is because free growth factors have short half-lives in plasma, making direct injection inefficient. Many growth factors are anchored and protected by sulfated glycosaminoglycans in the body. We set out to explore the use of heparin, a well-characterized sulfated glycosaminoglycan, for the controlled release of fibroblast growth factor-2 (FGF-2). Heparin binds a multitude of growth factors and maintains their bioactivity for an extended period of time. We used a biocompatible polycation to precipitate out the [heparin∶FGF-2] complex from neutral buffer to form a release matrix. We can control the release rate of FGF-2 from the resultant matrix by altering the molecular weight of the polycation. The FGF-2 released from the delivery complex maintained its bioactivity and initiated cellular responses that were at least as potent as fresh bolus FGF-2 and fresh heparin stabilized FGF-2. This new delivery platform is not limited to FGF-2 but applicable to the large family of heparin-binding growth factors.     

The Neurophysiology of Language Processing Shapes the Evolution of Grammar: Evidence from Case Marking

Do principles of language processing in the brain affect the way grammar evolves over time or is language change just a matter of socio-historical contingency? While the balance of evidence has been ambiguous and controversial, we identify here a neurophysiological constraint on the processing of language that has a systematic effect on the evolution of how noun phrases are marked by case (i.e. by such contrasts as between the English base form she and the object form her). In neurophysiological experiments across diverse languages we found that during processing, participants initially interpret the first base-form noun phrase they hear (e.g. she…) as an agent (which would fit a continuation like … greeted him), even when the sentence later requires the interpretation of a patient role (as in … was greeted). We show that this processing principle is also operative in Hindi, a language where initial base-form noun phrases most commonly denote patients because many agents receive a special case marker ("ergative") and are often left out in discourse. This finding suggests that the principle is species-wide and independent of the structural affordances of specific languages. As such, the principle favors the development and maintenance of case-marking systems that equate base-form cases with agents rather than with patients. We confirm this evolutionary bias by statistical analyses of phylogenetic signals in over 600 languages worldwide, controlling for confounding effects from language contact. Our findings suggest that at least one core property of grammar systematically adapts in its evolution to the neurophysiological conditions of the brain, independently of socio-historical factors. This opens up new avenues for understanding how specific properties of grammar have developed in tight interaction with the biological evolution of our species.     

Compliance Mixture Modelling with a Zero‐Effect Complier Class and Missing Data

Summary Randomized experiments are the gold standard for evaluating proposed treatments. The intent to treat estimand measures the effect of treatment assignment, but not the effect of treatment if subjects take treatments to which they are not assigned. The desire to estimate the efficacy of the treatment in this case has been the impetus for a substantial literature on compliance over the last 15 years. In papers dealing with this issue, it is typically assumed there are different types of subjects, for example, those who will follow treatment assignment (compliers), and those who will always take a particular treatment irrespective of treatment assignment. The estimands of primary interest are the complier proportion and the complier average treatment effect (CACE). To estimate CACE, researchers have used various methods, for example, instrumental variables and parametric mixture models, treating compliers as a single class. However, it is often unreasonable to believe all compliers will be affected. This article therefore treats compliers as a mixture of two types, those belonging to a zero‐effect class, others to an effect class. Second, in most experiments, some subjects drop out or simply do not report the value of the outcome variable, and the failure to take into account missing data can lead to biased estimates of treatment effects. Recent work on compliance in randomized experiments has addressed this issue by assuming missing data are missing at random or latently ignorable. We extend this work to the case where compliers are a mixture of types and also examine alternative types of nonignorable missing data assumptions.     

Factors of activation and stabilization of DNA-methylases from Shigella sonnei 47 and Mycobacterium smegmatis butyricum cells

A comparative study of factors of activation and stabilization of individual DNA-methylases from two bacterial strains--Shigella sonnei 47 and Mycobacterium smegmatis butyricum--isolated by isoelectrofocusing in a pH gradient has been carried out. Storage of enzymes at +4 degrees C (pH 7.5) is accompanied by periodic changes in the methylating activity. No such changes are observed when the enzymes are stored at pI of the protein. In this case the methylases with alkaline or close to neutral values of pI remain stable over a period of at least two weeks, whereas acidic proteins are irreversibly inactivated by the end of a two-week period. A stabilizing effect of BSA on DNA-methylases of Sso 47 and Mbu strains has been demonstrated. A direct correlation between the stabilizing effect of BSA and the degree of enzyme purity has been established. Ca2+ appear to be a universal activator of methylases of the above strains; these cations produce a potent, although a short-term effect and can be used in the production of enzyme preparations with a high specific activity in DNA recombinant technology. Protease inhibitors do not exert any appreciable effect on the methylase activity upon storage. Storage at -20 degrees C and at neutral pH leads to complete inactivation of all DNA-methylases within 24 hours. In this case glycerol is fairly ineffective as a stabilizing agent.     

A method for assessing factors influencing'false check'formation in fish scales

Scales are widely used to determine both the growth rates and the age of fish. Their use in this method of scale reading is however complicated by the occurrence of false checks. It has been difficult to investigate the particular environmental factors that normally cause these interruptions in growth because it usually takes many weeks before a check can be detected and the growing scale is a complex system. A technique has therefore been devised in which a scale is isolated from the fish and used to measure its metabolism of radioactive glycine. This gives a measure of protein synthesis which correlates well with the normal growth of the scale and of the whole fish. It is, however, a measurement of the'instantaneous growth rate'of the fish instead of one compounded over a long period of time and it thus opens up the possibility of investigating specific environmental factors that might cause changes in growth. The effects of handling, low oxygen levels, starvation, light and temperature changes have been studied by this technique. It has been shown that handling has the most marked effect but that oxygen levels and starvation also have direct effects that could induce false checks.     

Nuclear export of the glucocorticoid receptor is accelerated by cell fusion-dependent release of calreticulin

Nucleocytoplasmic exchange of nuclear hormone receptors is hypothesized to allow for rapid and direct interactions with cytoplasmic signaling factors. In addition to recycling between a na?ve, chaperone-associated cytoplasmic complex and a liganded chaperone-free nuclear form, the glucocorticoid receptor (GR) has been observed to shuttle between nucleus and cytoplasm. Nuclear export of GR and other nuclear receptors has been proposed to depend on direct interactions with calreticulin, which is predominantly localized to the lumen of the endoplasmic reticulum. We show that rapid calreticulin-mediated nuclear export of GR is a specific response to transient disruption of the endoplasmic reticulum that occurs during polyethylene glycol-mediated cell fusion. Using live and digitonin-permeabilized cells we demonstrate that, in the absence of cell fusion, GR nuclear export occurs slowly over a period of many hours independent of direct interaction with calreticulin. Our findings temper expectations that nuclear receptors respond rapidly and directly to cytoplasmic signals in the absence of additional regulatory control. These results highlight the importance of verifying findings of nucleocytoplasmic trafficking using techniques in addition to heterokaryon cell fusion.     

Plant DNA barcodes and the influence of gene flow

Success of species assignment using DNA barcodes has been shown to vary among plant lineages because of a wide range of different factors. In this study, we confirm the theoretical prediction that gene flow influences species assignment with simulations and a literature survey. We show that the genome experiencing the highest gene flow is, in the majority of the cases, the best suited for species delimitation. Our results clearly suggest that, for most angiosperm groups, plastid markers will not be the most appropriate for use as DNA barcodes. We therefore advocate shifting the focus from plastid to nuclear markers to achieve an overall higher success using DNA barcodes.     

Effects of Transcranial Direct Current Stimulation on the Control of Finger Force during Dexterous Manipulation in Healthy Older Adults

The contribution of poor finger force control to age-related decline in manual dexterity is above and beyond ubiquitous behavioral slowing. Altered control of the finger forces can impart unwanted torque on the object affecting its orientation, thus impairing manual performance. Anodal transcranial direct current stimulation (tDCS) over primary motor cortex (M1) has been shown to improve the performance speed on manual tasks in older adults. However, the effects of anodal tDCS over M1 on the finger force control during object manipulation in older adults remain to be fully explored. Here we determined the effects of anodal tDCS over M1 on the control of grip force in older adults while they manipulated an object with an uncertain mechanical property. Eight healthy older adults were instructed to grip and lift an object whose contact surfaces were unexpectedly made more or less slippery across trials using acetate and sandpaper surfaces, respectively. Subjects performed this task before and after receiving anodal or sham tDCS over M1 on two separate sessions using a cross-over design. We found that older adults used significantly lower grip force following anodal tDCS compared to sham tDCS. Friction measured at the finger-object interface remained invariant after anodal and sham tDCS. These findings suggest that anodal tDCS over M1 improved the control of grip force during object manipulation in healthy older adults. Although the cortical networks for representing objects and manipulative actions are complex, the reduction in grip force following anodal tDCS over M1 might be due to a cortical excitation yielding improved processing of object-specific sensory information and its integration with the motor commands for production of manipulative forces. Our findings indicate that tDCS has a potential to improve the control of finger force during dexterous manipulation in older adults.     

How a lateralized brain supports symmetrical bimanual tasks

A large repertoire of natural object manipulation tasks require precisely coupled symmetrical opposing forces by both hands on a single object. We asked how the lateralized brain handles this basic problem of spatial and temporal coordination. We show that the brain consistently appoints one of the hands as prime actor while the other assists, but the choice of acting hand is flexible. When study participants control a cursor by manipulating a tool held freely between the hands, the left hand becomes prime actor if the cursor moves directionally with the left-hand forces, whereas the right hand primarily acts if it moves with the opposing right-hand forces. In neurophysiological (electromyography, transcranial magnetic brain stimulation) and functional magnetic resonance brain imaging experiments we demonstrate that changes in hand assignment parallels a midline shift of lateralized activity in distal hand muscles, corticospinal pathways, and primary sensorimotor and cerebellar cortical areas. We conclude that the two hands can readily exchange roles as dominant actor in bimanual tasks. Spatial relationships between hand forces and goal motions determine hand assignments rather than habitual handedness. Finally, flexible role assignment of the hands is manifest at multiple levels of the motor system, from cortical regions all the way down to particular muscles.     

Mechanism of case processing in the brain: an FMRI study

In sentence comprehension research, the case system, which is one of the subsystems of the language processing system, has been assumed to play a crucial role in signifying relationships in sentences between noun phrases (NPs) and other elements, such as verbs, prepositions, nouns, and tense. However, so far, less attention has been paid to the question of how cases are processed in our brain. To this end, the current study used fMRI and scanned the brain activity of 15 native English speakers during an English-case processing task. The results showed that, while the processing of all cases activates the left inferior frontal gyrus and posterior part of the middle temporal gyrus, genitive case processing activates these two regions more than nominative and accusative case processing. Since the effect of the difference in behavioral performance among these three cases is excluded from brain activation data, the observed different brain activations would be due to the different processing patterns among the cases, indicating that cases are processed differently in our brains. The different brain activations between genitive case processing and nominative/accusative case processing may be due to the difference in structural complexity between them.     

The one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud

Assignment of an individual to the population from which it most probably originated based on its multilocus genotype has been widely applied in recent years. In this study, individual assignment based on microsatellite data was used to identify a case of fishing competition fraud. Despite the fact that the true population of origin was most probably not among the reference populations, recent modifications of the assignment tests were used in confidently excluding (p < 0.0001) the possibility of a 5.5 kg salmon (Salmo salar) originating from the fishing competition location, Lake Saimaa (south-east Finland). In fact, the probability of the suspect salmon originating from one of the regions that supply most of Finland's fish markets was found to be over 600 times higher than it originating from Lake Saimaa. When presented with this evidence, the offender confessed to purchasing the salmon at a local fish shop and criminal charges were laid. This study emphasizes the potential practical application of the individual assignment procedure, in particular the usefulness of confidently excluding populations as the origin of an individual. A similar strategy could be also used, for example in suspected cases of illegal poaching, in order to assign or exclude individuals from originating from a claimed population.     

Partial purification of a 5.7K glycoprotein from bovine vitreous which inhibits both angiogenesis and collagenase activity

An inhibitor of angiogenic activity similar to that described by Raymond and Jacobson (1) has been partially purified and shown to be a glycoprotein of molecular mass 5,700. This inhibitor gave rise to an avascular zone on the chick vitelline plexus and also negated the action of a low Mr angiogenic factor. When the angiogenic inhibitor was incubated with mammalian collagenase it inhibited the enzyme activity by nearly 70%. The relevance of these findings to the role of collagenase in angiogenesis is discussed.     

Imaging in five dimensions: time-dependent membrane potentials in individual mitochondria.

Because of its importance in the chemiosmotic theory, mitochondrial membrane potential has been the object of many investigations. Significantly, however, quantitative data on how energy transduction might be regulated or perturbed by the physiological state of the cell has only been gathered via indirect studies on isolated mitochondrial suspensions; quantitative studies on individual mitochondria in situ have not been possible because of their small size, their intrinsic motility, and the absence of appropriate analytical reagents. In this article, we combine techniques for rapid, high resolution, quantitative three-dimensional imaging microscopy and mathematical modeling to determine accurate distributions of a potentiometric fluorescent probe between the cytosol and individual mitochondria inside a living cell. Analysis of this distribution via the Nernst equation permits assignment of potentials to each of the imaged mitochondrial membranes. The mitochondrial membrane potentials are distributed over a narrow range centered at -150 mV within the neurites of differentiated neuroblastoma cells. We find that the membrane potential of a single mitochondrion is generally remarkably stable over times of 40-80 s, but significant fluctuations can occasionally be seen. The motility of individual mitochondria is not directly correlated to membrane potential, but mitochondria do become immobile after prolonged treatment with respiratory inhibitors or uncouplers. Thus, three spatial dimensions, a key physiological parameter, and their changes over time are all quantitated for objects at the resolution limit of light microscopy. The methods described may be readily extended to permit investigations of how mitochondrial function is integrated with other processes in the intact cell.     

Piecing together the structure-function puzzle: experiences in structure-based functional annotation of hypothetical proteins

The combination of genomic sequencing with structural genomics has provided a wealth of new structures for previously uncharacterized ORFs, more commonly referred to as hypothetical proteins. This rapid growth has been the direct result of high-throughput, automated approaches in both the identification of new ORFs and the determination of high-resolution 3-D protein structures. A significant bottleneck is reached, however, at the stage of functional annotation in that the assignment of function is not readily automatable. It is often the case that the initial structural analysis at best indicates a functional family for a given hypothetical protein, but further identification of a relevant ligand or substrate is impeded by the diversity of function in a particular structural classification of proteins family, a highly selective and specific ligand-binding site, or the identification of a novel protein fold. Our approach to the functional annotation of hypothetical proteins relies on the combination of structural information with additional bioinformatics evidence garnered from operon prediction, loose functional information of additional operon members, conservation of catalytic residues, as well as cocrystallization trials and virtual ligand screening. The synthesis of all available information for each protein has permitted the functional annotation of several hypothetical proteins from Escherichia coli and each assignment has been confirmed through generally accepted biochemical methods.     

Affiliation promotes the transmission of a social custom: handclasp grooming among captive chimpanzees

Handclasp grooming is a unique social custom, known to occur regularly among some, but not all populations of chimpanzees (Pan troglodytes). As with other cultural behaviors, it is assumed that this distinctive grooming posture is learned socially by one individual from another. However, statistical comparisons among factors thought to influence how a behavior spreads within a group have never, to our knowledge, been conducted. In the present study, the origination and spread of handclasp grooming in a group of captive chimpanzees was followed throughout more than 1,500 h of observation over a period of 12 years. We report on the frequency, bout duration, and number and demography of performers throughout the study period, and compare these findings to those reported for wild populations. We predicted that dyads with strong affiliative ties, measured by time spent in proximity to and grooming one another, were likely to develop a handclasp grooming partnership during the study period. A quadratic assignment procedure was used to compare correlations among observed frequencies of grooming and proximity with handclasp grooming in all possible dyads within the group. As predicted, the formation of new handclasp grooming dyads was positively correlated with the rate of overall grooming and proximity within a dyad. In addition, in nearly all dyads formed, at least one individual had been previously observed to handclasp groom. We concluded that affiliation and individual experience determines the transmission of handclasp grooming among captive chimpanzees.     

Depth-dependant response to light of the reef building coral, Pocillopora verrucosa: Implication of oxidative stress

Several environmental factors have been described to trigger bleaching in cnidarian/dinoflagellate endosymbiosis. However, the molecular mechanisms underlying this process still need more investigations. Symbiosis breakdown is known to result from physiological damage to animal host cells and/or symbionts. Cellular oxidation appears to be an essential player in this damage. Indeed, oxidative stress is a direct consequence of increase in irradiance and temperature, the two main environmental factors involved in bleaching. In this study, we examined the role of irradiance in inducing dissociation and oxidative stress in cnidarians and dinoflagellates. We used the bleaching-sensitive scleractinian coral Pocillopora verrucosa in a field cross-transplantation experiment performed between 5 m and 20 m depth at Grande Glorieuse Island (Indian Ocean), a preserved area subject to minimal anthropogenic influence. Cellular damage and increase in antioxidant defense were correlated with bleaching in upward transplanted samples. Downward transplanted colonies presented no associated alterations similar to the controls. We therefore conclude that increasing light induced bleaching via a prooxidative period. Remarkably, the distribution of Symbiodinium over depth was invariant; all colonies were monomorph for clade C, suggesting that bleaching sensitivity of P. verrucosa might not be associated with clade specificity.     

Modulation of Arm Reaching Movements during Processing of Arm/Hand-Related Action Verbs with and without Emotional Connotation

The theory of embodied language states that language comprehension relies on an internal reenactment of the sensorimotor experience associated with the processed word or sentence. Most evidence in support of this hypothesis had been collected using linguistic material without any emotional connotation. For instance, it had been shown that processing of arm-related verbs, but not of those leg-related verbs, affects the planning and execution of reaching movements; however, at present it is unknown whether this effect is further modulated by verbs evoking an emotional experience. Showing such a modulation might shed light on a very debated issue, i.e. the way in which the emotional meaning of a word is processed. To this end, we assessed whether processing arm/hand-related verbs describing actions with negative connotations (e.g. to stab) affects reaching movements differently from arm/hand-related verbs describing actions with neutral connotation (e.g. to comb). We exploited a go/no-go paradigm in which healthy participants were required to perform arm-reaching movements toward a target when verbs expressing emotional hand actions, neutral hand actions or foot actions were shown, and to refrain from moving when no-effector-related verbs were presented. Reaction times and percentages of errors increased when the verb involved the same effector as used to give the response. However, we also found that the size of this interference decreased when the arm/hand-related verbs had a negative emotional connotation. Crucially, we show that such modulation only occurred when the verb semantics had to be retrieved. These results suggest that the comprehension of negatively valenced verbs might require the simultaneous reenactment of the neural circuitry associated with the processing of the emotion evoked by their meaning and of the neural circuitry associated with their motor features.     

Proton-coupled electron transfer in Fe-superoxide dismutase and Mn-superoxide dismutase

Fe-containing superoxide dismutase (FeSOD) and MnSOD are widely assumed to employ the same catalytic mechanism. However this has not been completely tested. In 1985, Bull and Fee showed that FeSOD took up a proton upon reduction [J. Am. Chem. Soc. 107 (1985) 3295]. We now demonstrate that MnSOD incorporates the same crucial coupling between electron transfer and proton transfer. The redox-coupled H(+) acceptor has been presumed to be the coordinated solvent molecule, in both FeSOD and MnSOD, however this is very difficult to test experimentally. We have now examined the most plausible alternative: that Tyr34 accepts a proton upon SOD reduction. We report specific incorporation of 13C in the C(zeta) positions of Tyr residues, assignment of the C(zeta) signal of Tyr34 in each of oxidized FeSOD and MnSOD, and direct NMR observations showing that in both cases, Tyr34 is in the neutral protonated state. Thus Tyr34 cannot accept a proton upon SOD reduction, and coordinated solvent is concluded to be the redox-coupled H(+) acceptor instead, in both FeSOD and MnSOD. We have also confirmed by direct 13C observation that the pK of 8.5 of reduced FeSOD corresponds to deprotonation of Tyr34. This work thus provides experimental proof of important commonalities between the detailed mechanisms of FeSOD and MnSOD.