Relating middle-ear acoustic performance to body size in the cat family: measurements and models

Is the acoustic performance of the mammalian middle ear dependent on body size? We focus on the cat family, because of its qualitatively uniform (and distinctive) middle-ear structure, large size range, and the extensive data available from domestic cats which provide a framework for relating middle-ear acoustics to structure. We report measurements of acoustic admittance in 17 live adult ears of 11 exotic species, ranging in size from sand cat (3?kg) to tiger (180?kg). For low frequencies, the middle-ear response is compliant for all species and generally increases with size. The compliance of the middle-ear air space increases with size, but the compliance of the tympanic membrane and ossicular chain is not correlated with size. Structure-based rules are developed to represent some features of middle-ear performance: (1) low-frequency sensitivity increases with size; and (2) the frequency of a prominent notch in admittance decreases with size. Although some species deviate from the rules, the data generally support the idea that in larger felids the middle-ear response is shifted to lower frequencies. Thus, in the cat family, body size partly describes variations in auditory features. More speculatively, ethological pressures which might influence hearing performance are discussed.     

Ant-plant-homopteran mutualism: how the third partner affects the interaction between a plant-specialist ant and its myrmecophyte host

By estimating relative costs and benefits, we explored the role of the homopteran partner in the protection mutualism between the myrmecophyte Leonardoxa africana T3, the ant Aphomomyrmex afer, and sap-sucking homopterans tended by ants in the tree''s swollen hollow twigs. The ants obtain nest sites and food from their host-plant (food is obtained either directly by extrafloral nectar or indirectly via homopterans). Aphomomyrmex workers patrol the young leaves of L. africana T3 and protect them against phytophagous insects. Because ants tended, either solely or primarily, coccids in some trees and pseudococcids in others, we were able to study whether the nature of the interaction was dependent on the identity of the third partner. First, the type of homopteran affects the benefits to the tree of maintaining a large ant colony. Larger colony size (relative to tree size) confers greater protection against herbivory; this relationship is more pronounced for trees whose ants tend pseudococcids than for those in which ants tend coccids. Second, for trees (and associated ant colonies) of comparable size, homopteran biomass was much larger in trees harbouring coccids than in trees with pseudococcids. Thus, the cost to the tree of maintaining ants may be greater when ants are associated with coccids. The net benefits to the plant of maintaining ants appear to be much greater with pseudococcids as the third partner. To explore how the type of homopteran affects functioning of the system, we attempted to determine which of the resources (nest sites, extrafloral nectar, and homopterans) is likely to limit ant colony size. In trees where ants tended coccids, ant-colony biomass was strongly dependent on the number of extrafloral nectaries. In contrast, in trees whose ants tended only pseudococcids, colony biomass was not related to the number of nectaries and was most strongly determined by the volume of available nest sites. We present hypotheses to explain how the type of homopteran affects functioning of this symbiosis, and discuss the implications of our study for the evolutionary ecology of ant–plant–homopteran relationships.     

Student exam performance in flipped classroom sections is similar to that in active learning sections,and satisfaction with the flipped classroom hinges on attitudes toward learning from videos

ABSTRACT

The flipped classroom is a teaching innovation in which instructional content is delivered out of the classroom, often via videos, and the class period is used for application of the course material. While the popularity of the flipped classroom is growing exponentially, its benefits have not been extensively studied. In this study we compared three semesters of an undergraduate Genetics course that was non-flipped, but included a significant amount of active learning, to three semesters of a flipped course with the same content. Student exam performance was not statistically different between the active non-flipped and the flipped courses, suggesting that the benefits of the flipped environment may be similar to those achieved via active learning. We also examined student attitudes toward the flipped classroom, and found 56% of students were satisfied, 39% were dissatisfied, and 5% were neutral toward the flipped classroom. Our survey revealed that the clearest defining characteristic of dissatisfied students was not a dislike of classroom active learning activities. Rather, dissatisfied students disproportionately disliked, and had difficulty learning the course material, from videos.     

Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity.

An unexpected structural similarity is described between the pleckstrin homology (PH) domain and verotoxin. This similarity has escaped detection primarily due to the differences in topology that exist between the two proteins. By comparing this result with two previously reported similarities for the PH domain, one with the lipocalins and another with the FK506 binding protein, we discuss the problems of measuring and assessing structural similarities.     

Molecular diagnosis on tissues and cells: how it affects training and will affect practice in the future

C. Boyd and D. P. Boyle Molecular diagnosis on tissues and cells: how it affects training and will affect practice in the future On 25th November 2011, a symposium organized by the Royal College of Pathologists, entitled 'Molecular diagnosis on tissues and cells', took place in London. As trainees in histopathology and cytopathology, we were stimulated to consider the role that molecular biology is likely to play in future practice and how this is addressed by our own training. The symposium provided a basis for this article. Routine samples requiring molecular analysis are equally relevant to histopathologists and cytopathologists, and molecular biology laboratories are now using cytological as well as histological material for diagnostic testing, allowing different specimen types to be used as and when they are most appropriate. The most widely used types of molecular analysis in routine cellular pathology are EGFR testing in lung cancer, molecular testing of thyroid nodules, fluorescence in?situ hybridization testing of urine samples, clonality analysis in lymphoma testing, HER2 testing in breast and gastric cancer, KRAS testing in colorectal cancer, intraoperative assessment of breast cancer sentinel nodes, molecular testing of gastrointestinal stromal tumours and mismatch repair protein analysis. Of these, the majority in the UK are carried out on histopathology samples, although many are applicable to cytological samples if adequate material is obtained. We are particularly encouraged by the potential of molecular diagnostic cytology in traditionally difficult areas, such as intraoperative assessment. We believe that increasing reliance on molecular diagnostic techniques will also herald changes in training.     

Human Menkes X-chromosome disease and the staphylococcal cadmium-resistance ATPase: a remarkable similarity in protein sequences

A search with the proposed amino acid translation product from the new ‘candidate gene’ for human Menkes disease against protein sequence libraries showed a remarkable similarity to that for the cadmium efflux ATPase from Staphylococcus aureus resistance plasmids. The Menkes sequence appears closer to the CadA Cd²⁺ sequence than to P-type ATPases from animal sources. Menkes syndrome is an X-chromosome invariably fatal disease that results from abberant copper metabolism. The gene that is defective in Menkes patients, i.e. the Menkes candidate gene, encodes a P-type ATPase, whose properties satisfactorily explain the phenotype of the disease. P-type ATPases are all cation pumps, either for uptake (e.g. the bacterial Kdp K⁺ ATPase), for efflux (e.g. the muscle sarcoplasmic reticulum Ca²⁺ ATPase), or for cation exchange (e.g. the animal cell Na⁺/K⁺ ATPase). These enzymes have a conserved aspartate residue that is transiently phosphorylated from ATP during the transport cycle, hence the name ‘P-type’ ATPase. The Menkes sequence shares with the staphylococcal CadA ATPase those regions common to all P-type ATPases and also an N-terminal dithiol region that was proposed to be a ‘metal-binding motif’. There are one or two copies of this motif in the available CadA sequences and six copies in the Menkes sequence.     

How the length of genital parts affects copulation performance in a carabid beetle: implications for correlated genital evolution between the sexes

To identify factors leading to the correlated evolution of exaggerated male and female genitalia, we studied the effects of the variable dimensions of corresponding functional genital parts (male copulatory piece and female vaginal appendix) on copulatory performance in the polygamous carabid beetle Carabus (Ohomopterus) maiyasanus. We used mating pairs of individuals from two populations to increase the variances in genital dimensions and determined the copulation performance (insemination and spermatophore replacement, and copulation time) in single‐ and double‐mating situations. In single mating, insemination success was not affected by genital dimensions, although the copulation time was significantly shorter when the male aedeagus was longer. In the double‐mating experiment, insemination and replacement of spermatophores by the second male succeeded more frequently when the copulatory piece was shorter and the vaginal appendix was longer, and when the difference between the length of the copulatory piece and the vaginal appendix was smaller. Thus, a matching of the corresponding genital parts between the sexes increases the male's reproductive success in sperm competition, but elongation of the copulatory piece cannot be explained simply by the improvement in male reproductive success. We discuss possible factors for the elongation of genital parts in terms of sexual conflict and reproductive interference through interspecific copulation.     

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation

MOTIVATION: Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientific natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or 'semantic similarity' between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses. RESULTS: We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases. AVAILABILITY: Software available from http://www.russet.org.uk.     

Multiple stressors: using the honeybee model BEEHAVE to explore how spatial and temporal forage stress affects colony resilience

The causes underlying the increased mortality of honeybee Apis mellifera colonies observed over the past decade remain unclear. Since so far the evidence for monocausal explanations is equivocal, involvement of multiple stressors is generally assumed. We here focus on various aspects of forage availability, which have received less attention than other stressors because it is virtually impossible to explore them empirically. We applied the colony model BEEHAVE, which links within‐hive dynamics and foraging, to stylized landscape settings to explore how foraging distance, forage supply, and “forage gaps”, i.e. periods in which honeybees cannot find any nectar and pollen, affect colony resilience and the mechanisms behind. We found that colony extinction was mainly driven by foraging distance, but the timing of forage gaps had strongest effects on time to extinction. Sensitivity to forage gaps of 15 days was highest in June or July even if otherwise forage availability was sufficient to survive. Forage availability affected colonies via cascading effects on queen's egg‐laying rate, reduction of new‐emerging brood stages developing into adult workers, pollen debt, lack of workforce for nursing, and reduced foraging activity. Forage gaps in July led to reduction in egg‐laying and increased mortality of brood stages at a time when the queen's seasonal egg‐laying rate is at its maximum, leading to colony failure over time. Our results demonstrate that badly timed forage gaps interacting with poor overall forage supply reduce honeybee colony resilience. Existing regulation mechanisms which in principle enable colonies to cope with varying forage supply in a given landscape and year, such as a reduction in egg‐laying, have only a certain capacity. Our results are hypothetical, as they are obtained from simplified landscape settings, but they are consistent with existing empirical knowledge. They offer ample opportunities for testing the predicted effects of forage stress in controlled experiments.     

Timing of disturbance and vegetation development: how sowing date affects the weed flora in spring‐sown crops

Abstract. The number of annual weeds were recorded in 752 field experiments in spring‐sown cereal crops conducted in Sweden 1972–1993. Two null hypotheses were tested regarding how the sowing date influenced the weed flora. 1. There is no relationship between the weed flora composition and sowing date. A pCCA (with geographic regions, crop species and soil types as covariables) clearly refuted this hypothesis. Hence, the composition of the weed flora varied depending on sowing date. 2. Species classified as summer annuals, winter annuals and germination generalists (that can germinate substantially in both spring and autumn) do not differ in their placement along the first ordination axis in the pCCA, i.e. according to sowing date. An ANOVA was unable to reject this hypothesis. Hence, germination syndrome classification did not explain the observed community differences related to sowing date. These results illustrate the importance of the date of disturbance for any secondary succession involving a seed bank and also the importance of annual dormancy cycles in seed banks.     

The teacher, the physician and the person: how faculty's teaching performance influences their role modelling

Objective

Previous studies identified different typologies of role models (as teacher/supervisor, physician and person) and explored which of faculty''s characteristics could distinguish good role models. The aim of this study was to explore how and to which extent clinical faculty''s teaching performance influences residents'' evaluations of faculty''s different role modelling statuses, especially across different specialties.

Methods

In a prospective multicenter multispecialty study of faculty''s teaching performance, we used web-based questionnaires to gather empirical data from residents. The main outcome measures were the different typologies of role modelling. The predictors were faculty''s overall teaching performance and faculty''s teaching performance on specific domains of teaching. The data were analyzed using multilevel regression equations.

Results

In total 219 (69% response rate) residents filled out 2111 questionnaires about 423 (96% response rate) faculty. Faculty''s overall teaching performance influenced all role model typologies (OR: from 8.0 to 166.2). For the specific domains of teaching, overall, all three role model typologies were strongly associated with “professional attitude towards residents” (OR: 3.28 for teacher/supervisor, 2.72 for physician and 7.20 for the person role). Further, the teacher/supervisor role was strongly associated with “feedback” and “learning climate” (OR: 3.23 and 2.70). However, the associations of the specific domains of teaching with faculty''s role modelling varied widely across specialties.

Conclusion

This study suggests that faculty can substantially enhance their role modelling by improving their teaching performance. The amount of influence that the specific domains of teaching have on role modelling differs across specialties.     

Dry versus wet and gross: Comparisons between the dry skull method and gross dissection in estimations of jaw muscle cross-sectional area and bite forces in sea otters

Bite force is a measure of feeding performance used to elucidate links between animal morphology, ecology, and fitness. Obtaining live individuals for in vivo bite-force measurements or freshly deceased specimens for bite force modeling is challenging for many species. Thomason's dry skull method for mammals relies solely on osteological specimens and, therefore, presents an advantageous approach that enables researchers to estimate and compare bite forces across extant and even extinct species. However, how accurately the dry skull method estimates physiological cross-sectional area (PCSA) of the jaw adductor muscles and theoretical bite force has rarely been tested. Here, we use an ontogenetic series of southern sea otters (Enhydra lutris nereis) to test the hypothesis that skeletomuscular traits estimated from the dry skull method accurately predicts test traits derived from dissection-based biomechanical modeling. Although variables from these two methods exhibited strong positive relationships across ontogeny, we found that the dry skull method overestimates PCSA of the masseter and underestimates PCSA of the temporalis. Jaw adductor in-levers for both jaw muscles and overall bite force are overestimated. Surprisingly, we reveal that sexual dimorphism in craniomandibular shape affects temporalis PCSA estimations; the dry skull method predicted female temporalis PCSA well but underestimates male temporalis PCSA across ontogeny. These results highlight the importance of accounting for sexual dimorphism and other intraspecific variation when using the dry skull method. Together, we found the dry skull method provides an underestimation of bite force over ontogeny and that the underlying anatomical components driving bite force may be misrepresented.     

ADVANCE and ADAM: two algorithms for the analysis of global similarity between homologous informational sequences

Two algorithms for the analysis of global similarity betweensequences of informational polymeric molecules (nucleic acidsand proteins) are proposed: one (ADVANCE) merely gives a quantificationof the global similarity between two sequences, and is veryfast, the other (ADAM) also provides an alignment of the sequences.Both are new algorithms, implement Sellers' theorem, do notrequire parameters, are able to analyze two sequences of 32000 elements each, and are fast; nevertheless, they differ deeplyin the algorithm, in the programming language type, and in theirplanning, and will thus have to be treated separately. In fact,the different nature of the required output in each programcauses the common aim (to obtain power and speed) to be reachedonly through very different ways and methods.     

Grape variety affects larval performance and also female reproductive performance of the European grapevine moth Lobesia botrana (Lepidoptera: Tortricidae)

For insect herbivores, the quality of the larval host plant is a key determinant of fitness. Therefore, insect populations are supposed to be positively correlated with the nutritional quality of their host plant. This study aimed to determine if and how different varieties of grapes (including the wild grape Lambrusque) affect both larval and adult performance of the polyphagous European grapevine moth Lobesia botrana (Denis & Schiffermüller). Significant differences were found in larval development time, but not in pupal mass, adult emergence rate, or sex ratio. Although the fecundity of females is not different among varieties, females fed on some varieties produced eggs of different sizes which are correlated to their fertility. Thus, females adapt resource allocation to eggs depending on their diet as larvae. Using a fitness index, the average reproductive output was found to be highest for females reared on cv. Chardonnay. Females reared on wild grape produced a fitness index identical to the cultivated grapes. However, Lambrusque and Gewurztraminer separate themselves from the cultivated varieties according to our discriminant analyses. It is emphasized, through this study, that cultivars fed on by larvae should be considered in the population dynamics of L. botrana and that egg number is insufficient to determine host plant quality.     

Relationship between the weathering of clay minerals and the nitrification rate: a rapid tree species effect

We compared the properties of the clay mineral fraction and the composition of soil solutions in a Fagus sylvatica coppice (native forest) and four adjacent plantations of Pseudotsuga menziesii, Pinus nigra, Picea abies and Quercus sessiliflora planted in 1976. The results revealed changes of clay fraction properties due to tree species effect. Clay samples from Douglas fir and pine stands differ when compared to other species. Twenty-eight years after planting, we observed the following changes: a more pronounced swelling after citrate extraction and ethylene glycol solvation, a higher CEC and a smaller poorly crystallised aluminium content. All these changes affecting the clay fraction agreed well with soil solution analyses which revealed high NO₃ ^?, H⁺ and Al concentrations under Douglas fir and pine. These changes were explained by a strong net nitrification under Douglas fir and pine stands when compared with other tree species. The higher NO₃ ^? concentrations in soil solutions should be linked to the presence, type and activity of ammonia-oxiding bacteria which are likely influenced by tree species. The production of NO₃ ^? in excess of biological demand leads to a net production of hydrogen ion and enhances the dissolution of poorly crystallised Al-minerals. Secondary Al-bearing minerals constituted the principal acid-consuming system in these soils. As a consequence, the depletion of interlayer spaces of hydroxyinterlayered minerals increases the number of sites for exchangeable cation fixation and increases CEC of the clay fraction. The dissolution of Al oxy-hydroxides explain the increase in Al concentrations of soil solutions under Douglas fir and pine stands when compared to other species. Nitrate and dissolved aluminium were conjointly leached in the soil solutions. A change in environmental conditions, like an introduction of tree species, enough modifies soil processes to induce significant changes in the soil mineralogical composition even over a period of time as short as some tens of years. Generally, mineral weathering has been considered to be very slow and unlikely to change over tens of years, resulting in few studies capable of detecting changes in mineralogy. This study appears to have detected changes in clay mineralogy during a period of 28 years after the planting of forest species. Our study represents a single location with a limited block design, but causes us to conclude that the observed changes could be widely representative. Where available, archived samples should be utilized and long-term experiments set up so that similar changes can be tested for and detected using more robust designs. The plausible hypothesis we present to explain apparent changes in clay mineralogy has strong relevance to the sustainable management of land.     

Plant genotype and the preference and performance of herbivores: cultivar affects apple resistance to the florivorous weevil Anthonomus pomorum

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