Vision of the honeybee Apis mellifera for patterns with one pair of equal orthogonal bars

The visual discrimination of patterns of two equal orthogonal black bars by honeybees has been studied in a Y-choice apparatus with the patterns presented vertically at a fixed range. Previous work shows that bees can discriminate the locations of one, or possibly more, contrasts in targets that are in the same position throughout the training. Therefore, in critical experiments, the locations of areas of black were regularly shuffled to make them useless as cues. The bees discriminate consistent radial and tangential cues irrespective of their location on the target during learning and testing. Orientation cues, to be discriminated, must be presented on corresponding sides of the two targets. When orientation, radial and tangential cues are omitted or made useless by alternating them, discrimination is impossible, although the patterns may look quite different to us. The shape or the layout of local cues is not re-assembled from the locations of the bars, even when there are only two bars in the pattern, as if the bees cannot locate the individual bars within the large spatial fields of their global filters.     

Distinguishing between convergence and parallelism is central to comparative biology: a reply to Williams and Ebach

The definitions of character similarity, homology, homoplasy, heterology, parallelism and convergence are clarified in the framework of current phylogenetic methodology. They are all associated with definite patterns of character change and can consequently be tested by phylogeny building. Their crucial significance in comparative biology is illustrated using demonstrative examples. © The Willi Hennig Society 2006.     

Lifespan of Commodities,Part II

Lifespan of commodities is essential information for material flow analysis and material stock accounting. Lifespan data is available in the literature; however, it varies in definition and in methodology employed. This article reviews and categorizes different types of lifespan distribution and distribution estimation methodologies, and investigates the relationship and differences between lifespan definitions and estimation methodologies. Lifespan distribution of commodities can be classified into five types from two perspectives: base year for which the distribution is drawn, and vertical axis of the distribution. The methodologies for estimating lifespan distribution were classified into four types and the details of each methodology and the relationship to the definition of lifespan were also clarified. This article also examines differences in actual lifespan data—between the types of distribution, the definitions, and the employed methodologies—by comparing reported data in literature. Any of the four methodologies are theoretically applicable and provide the same value of a lifespan; however unless accurate data such as census statistics are available, lifespan data can vary, and therefore we must be very cautious about the representativeness of sample data.     

Bee vision of pattern and 3D. The Bidder Lecture 1994

Insect vision is nothing if not active. The regular head movements, called saccades, enable the fly Drosophila to keep a straight path in flight despite inequalities in the thrust of the wings. Using their own motion, bees in flight measure the ranges of nearby objects. A long history of research shows that bees discriminate visually in ways that depend on their activity or task, so we must distinguish between vision during flying, fixating or hovering and landing. Bees return again and again for a reward of sugar solution and use their eyes to find their way. In an apparatus that makes them discriminate between two simulataneously visible but regularly interchanged targets, seen at a distance of 27 cm, bees are able to distinguish a remarkable number of simple patterns, but they fail in certain critical cases. The results can be explained with the hypothesis that bees have several broadly tuned overlapping filters with large fields that respond to the predominant orientation in a region of the image, and others for radial and circular patterns. Together with colour, these filters are independent of range. Bees prefer to use landmarks where they can, then global pattern at the largest scale, and lastly the detail around the goal. The way that discrimination of one visual feature is independent of other variables can be explained by models analogous to the colour triangle in colour discrimination.     

Spatial patterns of cells in dividing epithelia.

The spatial patterns of cell boundaries in a view of the apical surface of a dividing epithelium are explored by constructing a hypothetical cell pattern of an epithelium of dividing cells. The two elements specified in the hypothetical pattern are the orientation of division planes and the separation between the division planes in neighbouring cells. The orientations of division planes in one generation are all the same but are orthogonal to those in the preceding generation. The division-plane orientations follow in an orthogonal succession, as happens in early embryos. The division planes in neighbouring cells are offset. The contractions of division planes that would occur during cytokinesis distort existing boundaries creating various types of cell shapes. The patterns generated resemble cell patterns found in life. The hypothetical pattern is regenerative and shows how epithelial cell patterns where cells divide might arise. It has enabled the putative identification of sister cells and first cousins in the embryonic chick chorion.     

Facing the Heat: Does Desiccation and Thermal Stress Explain Patterns of Orientation in an Intertidal Invertebrate?

A key challenge for ecologists is to quantify, explain and predict the ecology and behaviour of animals from knowledge of their basic physiology. Compared to our knowledge of many other types of distribution and behaviour, and how these are linked to individual function, we have a poor level of understanding of the causal basis for orientation behaviours. Most explanations for patterns of animal orientation assume that animals will modify their exposure to environmental factors by altering their orientation. We used a keystone grazer on rocky shores, the limpet Cellana tramoserica, to test this idea. Manipulative experiments were done to evaluate whether orientation during emersion affected limpet desiccation or body temperature. Body temperature was determined from infrared thermography, a technique that minimises disturbance to the test organism. No causal relationships were found between orientation and (i) level of desiccation and (ii) their body temperature. These results add to the growing knowledge that responses to desiccation and thermal stress may be less important in modifying the behaviour of intertidal organisms than previously supposed and that thermoregulation does not always reflect patterns of animal orientation. Much of what we understand about orientation comes from studies of animals able to modify orientation over very short time scales. Our data suggests that for animals whose location is less flexible, orientation decisions may have less to do with responses to environmental factors and more to do with structural habitat properties or intrinsic individual attributes. Therefore we suggest future studies into processes affecting orientation must include organisms with differing levels of behavioural plasticity.     

Testing the Accuracy of Different A-Axis Types for Measuring the Orientation of Bones in the Archaeological and Paleontological Record

Orientation of archaeological and paleontological materials plays a prominent role in the interpretation of site formation processes. Allochthony and authochthony are frequently assumed from orientation patterns or lack thereof. Although it is still debated to what extent orientation of items can be produced in original depositional contexts, the recent use of GIS tools to measure orientations has highlighted several ways of reproducing A-axes with which to address these taphonomic issues. In the present study, the three most relevant A-axis types are compared to test their accuracy in reproducing water current direction. Although results may be similar in specific bone shapes, differences are important in other shapes. As known in engineering working with wind and fluid mechanics (developing shape optimization), longitudinal symmetrical axes (LSA) are the one that best orient structures against or in the same direction of wind and water. The present work shows that this is also the case for bones (regardless of shape), since LSA produce the most accurate estimates of flow direction. This has important consequences for the interpretation of orientation patterns at sites, since this type of axis is still not properly reproduced by GIS available tools.     

Strong patterns of head orientation in Patella spp. of the UK

Patellogastropod limpets are a widespread and extensively studied taxa, and yet comparisons between species and geographic regions are rare; instead, results are often generalized across these differences. This study investigated patterns of head orientation in Patella species at four locations in the UK. The proportion of downwards facing limpets was also compared between areas in two locations with and without barnacles. Regardless of location, there was a strong downwards bias in orientation and the proportion of downwards facing limpets did not differ in the presence of barnacles. The results are compared with patterns of orientation exhibited by the Australian patellogastropod Cellana tramoserica; this suggests that malacologists should be more cautious in extrapolating patterns of behaviour and distribution between species of patellogastropods and across regions.     

Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target

Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all sidechains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the sidechains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins, which suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods.     

Kinematics of plant growth.

Many of the concepts and equations which have been used in the study of compressible fluids can be applied to problems of plant development. Growth field variables, i.e. functions of position in the plant and of time, can be specified in either Eulerian (spatial) or Lagrangian (material) terms. The two specifications coincide only when the spatial distribution of the variable is steady, and steady patterns are most likely to emerge when an apex is chosen as origin of the co-ordinate system. The growth field itself can be described locally by the magnitude and orientation of the principal axes of the rate of strain tensor and by the vorticity tensor. Material derivatives can be calculated if the temporal and spatial variation in both growth velocity, u (rate of displacement from a material origin), and the variable of interest are known. The equation of continuity shows the importance of including both growth velocity, u, and growth rate, ▽ ·u in estimates of local biosynthesis and transport rates in expanding tissue, although the classical continuity equation must be modified to accommodate the compartmentalized distributions characteristic of plant tissue. Relatively little information on spatial variation in plant organs can be found in the botanical literature, but the current availability of interactive computer graphics equipment suggests that analysis of the spatial distribution of growth rates at least is no longer difficult.     

Evolution of the Vertebrate Central Nervous System: Patterns and Processes

AS brains do not fossilize, most proposed phylogenetic sequencesfor central nervous system characters must be based on the patternsof variation of those characters in living organisms. Similarly,hypotheses regarding how brains change through time, and theevolutionary processes that produce these changes, are ultimatelybased on the character patterns recognized. It is critical inthese analyses to distinguish between homologous and homoplasouscharacters if errors in the reconstruction and interpretationof phylogenies are to be minimized. Definitions of homologyand homoplasy are reviewed, as are the concepts that bear ontheir application. Cladistic definitions are adopted, and criteriafor distinguishing homologous from homoplasous characters arediscussed. Analysis of a number of CNS characters that are usuallyassumed to be homologous reveals that homoplasous charactersappear among them. As in other organ systems, homoplasous charactersare actually common. A number of previous hypotheses regardingCNS evolution are reviewed in the context of new data on neuralconnections and their cladistic analysis. Some of these hypothesesmay be falsified by a cladistic treatment of CNS characters,whereas sufficient data do not exist to evaluate others.     

Backbone solution structures of proteins using residual dipolar couplings: Application to a novel structural genomics target

Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all sidechains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the sidechains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins, which suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods. This revised version was published online in March 2005 with corrections to the references.     

Approaches to trophic analysis of paleocommunities

Trophic analysis of communities consists of three methods: (1) measuring energy flow, (2) reconstructing food chains. and (3) describing feeding habit - substrate niche patterns. The latter two methods are useful in interpreting evolutionary patterns and depositional environments of paleocommunities. Because the preserved trophic structure may differ significantly from the actual structure. each study must test the hypothesis that preserved trophic structure is related to the environment. Analysis of several modem marine communities shows that their 'preserved' structure would not differ greatly from the actual structure. A comparison of some Holocene communities with Tertiary and Cretaceous communities shows that some communities from comparable environments have distinct feeding habit-substrate niche patterns. Differences can be explained by the evolutionary stage of the biosphere. Trophic structure seems to be partly related to over-all environmental stability, to food resources, and to substrate type.     

Development of orientation preference in the mammalian visual cortex.

Recent experiments have studied the development of orientation selectivity in normal animals, visually deprived animals, and animals where patterns of neuronal activity have been altered. Results of these experiments indicate that orientation tuning appears very early in development, and that normal patterns of activity are necessary for its normal development. Visual experience is not needed for early development of orientation, but is crucial for maintaining orientation selectivity. Neuronal activity and vision thus seem to play similar roles in the development of orientation selectivity as they do in the development of eye-specific segregation in the visual system.     

Measurement of visual channels by contrast adaptation.

Inspection of a high-contrast grating pattern affects our ability to detect patterns that are similar. This technique can be used to infer the underlying mechanisms of the visual system. By using this technique, measurements of the bandwidth of orientation channels are taken for different levels of adapting contrast and adapting duration. If the threshold elevation is plotted as the difference between the unadapted and adapted threshold in decibels, then the orientation bandwidth is invariant if taken at some fraction of the maximum elevation. This results from the fact that, as the orientation difference between the adapting and test patterns increases, the function relating threshold elevation to adapting contrast reduces in slope. These data contradict the often-used 'equivalent contrast transformation' (in which the fall off in the adaptation effect with respect to orientation is expressed in terms of an equivalent reduction in adapting contrast) as this would produce quite different bandwidths at different adapting contrasts. The data also address the issue of the neuronal mechanisms of adaptation.     

Spatial coincidence of cues in visual learning by the honeybee (Apis mellifera)

The discrimination of patterns was studied in a Y-choice chamber fitted with a transparent baffle in each arm, through which the bees had a choice of two targets via openings 5cm wide. The bees see the positive (rewarded) and the negative (unrewarded) targets from a fixed distance. The patterns were bars (subtending 22 degrees x5.4 degrees at the point of choice) presented in one-quarter of each target. The bars were moved to a different quarter of the target every 5min, to make the location of black useless as a cue. A coincident presentation is when the bar on the left target is on the same side of the target as the bar on the right target. The bees learn the orientation cue when the presentation is coincident but otherwise cannot learn it. This experiment shows that bees do not centre their attention on the individual bars, otherwise they would always discriminate the orientation. Centring the target as a whole precedes learning. Having learned with the bar on one side of the targets, bees do not recognize the same cue presented on the other side. A separate orientation cue can be learned on each side. A radial/tangential cue is preferred to a conflicting orientation cue.     

Terminology for contractions of muscles during shortening, while isometric, and during lengthening.

Communication among scientists must be clear and concise to avoid ambiguity and misinterpretations. The selection of words must be based on accepted definitions. The fields of biomechanics, muscle physiology, and exercise science have had a particularly difficult time with terminology, arising from the complexity of muscle contractions and by the use of inappropriate terminology by scientists. The dictionary definition of the verb "contract," specifically for the case of muscle, is "to undergo an increase in tension, or force, and become shorter." Under all circumstances, an activated muscle generates force, but an activated muscle generating force does not invariably shorten! During the 1920s and 1930s, investigators recognized that the interaction between the force generated by the muscle and the load on the muscle results in either shortening, no length change (isometric), or lengthening of the muscle. The recognition that muscles perform three different types of "contractions" required that contraction be redefined as "to undergo activation and generate force." Modifiers of contraction are then needed to clarify the lack of movement or the directionality of movement. Despite the contradiction, for 75 years the lack of movement has been termed an "isometric contraction." The directionality of the movement is then best described by the adjectives "shortening" and "lengthening." The definitions of "concentric" as "having the same center" and of "eccentric" as "not having the same center" are consistent with hypertrophy, or remodeling of the heart muscle, but are inappropriate to describe the contractions of skeletal muscles.     

Mitotic orientation in three dimensions determined from multiple projections.

The three-dimensional orientation of mitoses in mouse small intestinal crypts of Lieberkuhn was determined from multiple projections of the mitotic figures in whole mounts of isolated intestinal crypts. We found evidence of a significant orientational bias for mitoses whose daughter cells would be added along the long axis of the crypt, and thus conform to the maintenance of the cylindrical shape of the intestinal crypt. However, we also observed many mitoses whose progeny must be rearranged if the simple cylindrical shape of the intestinal crypt is to be maintained. Our results indicate that the ultimate behavior of progeny cells and hence of local tissue form may not strictly depend on the orientation of mitosis. The methods presented may also be used in the study of mitotic orientation in other tissues.     

基于生态位理论研究群落构建的方法进展

理解群落构建过程可以解释生物多样性格局的形成和维持,对于生物多样性保护起到关键作用。生态位理论是群落构建研究的核心框架之一。该理论认为群落构建是生物作用和非生物作用将区域物种库中的物种选入局域群落的确定过程。近年来,随着该领域受到的关注越来越多,研究者不但从物种、谱系或功能等生物多样性维度来研究群落构建,所使用的多样性指数、零模型算法和物种库界定方式等也多种多样。本文回顾了从生物多样性不同维度研究群落构建的优势与局限,总结了群落构建过程中构建零模型和界定物种库时需要注意的一些问题,介绍了部分群落构建研究的最新方法学进展和研究成果。最后,结合近年来的研究案例提出了对未来群落构建研究的一些建议。