Passive acoustic monitoring of the distribution patterns of Irrawaddy dolphins (Orcaella brevirostris) in the middle reaches of the Ayeyarwady River,Myanmar

The Irrawaddy dolphins (Orcaella brevirostris) are an endangered species. Thus, up-to-date information on the distribution pattern of dolphins is critical for its proper management and conservation. Using a towed passive acoustic monitoring device, the distribution pattern of the Irrawaddy dolphins in the middle reaches of the Ayeyarwady River, Myanmar, was investigated during a vessel-based survey between Mingun and Katha. This region was successively divided into segments 1–4 from upstream to downstream. Sixteen echolocation encounters, with a series of click trains separated by <8 min and 26 dolphin acoustic trajectories were recorded. The mean dolphin detection rate (animals/kilometer) across the four segments progressively increased from upstream to downstream. High relative abundance was observed in segment 4 (46%) and segment 1 (23%) which was consistent with findings from historical boat-based visual surveys. The averaged interclick intervals of each click train in segment 2 and 4 was significantly shorter than that in segment 3, indicating that the dolphins in these segments frequently use shorter-ranged biosonar. More frequent and consistent surveys with a systematic sampling track design that incorporates other factors and covering the whole distribution range along the Ayeyarwady River and at varied water levels are needed in the future.     

Variation in body segment number within and between populations of the centipede Strigamia maritima (Chilopoda: Geophilomorpha)

Although most arthropod species have a fixed number of body segments, one order of centipedes – the Geophilomorpha – provides an unusual opportunity to study the variation and microevolution of segment number. This is because all species in all but one family exhibit variation in the number of leg‐bearing segments (LBS) within and between natural populations. One species in particular, the coastal geophilomorph Strigamia maritima, has become a ‘model system’ for these studies, because of its high population densities and the consequent ease of collecting large samples. Previous studies on this species have examined various aspects of segment number variation. However, most studies have characterized each population by an LBS distribution and a mean LBS number that are based on data from all life‐stages. Here, we dissect the variation within as well as between populations and show that different cohorts within a population often have significantly different LBS number distributions. This is almost certainly due to developmental plasticity, probably related to the prevailing microhabitat temperature within brood chambers, but possibly related to other environmental factors too. Although we found no evidence of selection, the fact that different species of geophilomorphs have different LBS distributions suggests that, in the long term, selection may act on the developmental reaction norm of LBS number. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 678–685.     

Postembryonic development of Antygomonas incomitata (Kinorhyncha: Cyclorhagida)

Postembryonic development in the kinorhynch species Antygomonas incomitata was examined using scanning electron microscopy. The morphology of the six juvenile stages, J‐1 to J‐6, varies at numerous details, but they can also be distinguished by a few key characters. Juvenile stage 1 by its composition of only nine trunk segments; J‐2 by the combination of possessing 10 trunk segments, but no cuspidate spines on segment 9; J‐3 by the presence of cuspidate spines on segment 9, but only one pair of cuspidate spines on segment 8; J‐4 by the combination of 10 trunk segments only, but having two pairs of cuspidate spines on segment 8; J‐5 by possessing 11 trunk segments and same spine compositions as adults but is still maintaining postmarginal spiculae; J‐6 specimens closely resemble adults and are most easily identified by their reduced trunk lengths. New segments are formed in a growth zone in the anterior part of the terminal segment. The complete number of segments is reached in J‐5. Development of cuticular head and trunk structures are described through all postembryonic stages and following developmental patterns could be outlined: the mouth cone possesses outer oral styles from J‐1, but in J‐1 to J‐3, the styles alternate in size. Scalids of the introvert are added after each molt, and scalids appear earliest in the anterior rings, whereas scalids in more posterior rings are added in older postembryonic stages. The early J‐1 stage is poor in spines and sensory spots and both structures increase in number after each molt. The complete spine composition is reached in J‐4, whereas new sensory spots appear after all molts, inclusive the final one from J‐6 to adult. Sensory spots in the paraventral positions often appear as Type 3 sensory spots but are through development transformed to Type 2. This transformation happens earliest on the anterior segments. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.     

Extensive nerve overgrowth and paucity of the tailed asymmetric form (16 S) of acetylcholinesterase in the developing skeletal neuromuscular system of the dysgenic (mdg/mdg) mouse

Segmentation of the mesoderm in the head of a newt embryo is revealed by scanning electron microscopy. By the end of gastrulation, the newt embryo is already segmented from one end to the other, with additional segments added later by the tail bud. This metameric segmentation appears long before the first “somite” can be seen in the late neurula by light microscopy. The six segments found in the newt head look much like the six most-cranial segments described decades ago in shark embryos. Mesodermal segments in the newt head are similar to somitomeres in amniote embryos, but in amniote embryos, the numbers and relationships of head segments are quite different from those of the newt. In both amniote and newt, the first segment abuts the prosencephalon, but for each more caudal head segment, where the newt embryo has one segment, the amniote has two. Although the pattern and distribution of cranial neural crest is quite similar in newt and amniote embryos, there are different relationships between migrating crest masses and mesodermal segments due to the doubling of most of the cranial segments in amniotes. It now appears that all vertebrate embryos, regardless of their mode of gastrulation, form similar mesodermal segments from one end of the embryo to the other, and this metameric pattern is established during gastrulation.     

Diurnal migration of Echinostoma caproni (Digenea: Echinostomatidae) in ICR mice

Twenty-four female ICR mice, 12 acclimated to a 12 ∶ 12 light-dark cycle and 12 to a 12 ∶ 12 dark-light cycle for 7 days, were each infected with 10 metacercariae of Echinostoma caproni. Infected mice were maintained on their respective lighting regimes for 28 days. Six mice (3 from each group) were necropsied at 4-hr intervals beginning at 0700 hr. The small intestine was removed, opened, and the position of individual worms and worm clusters was measured to the nearest 0.1 cm. Each intestine was subsequently divided into 20 equal segments and individual worms and worm clusters were assigned to the appropriate segment based on the original measurements. All worms were found in the posterior 55% of the intestine (ileum). All posterior segments (10-20), with the exception of segment 18, harbored at least 1 worm at some time. A Monte Carlo simulation of worm abundance in segments 10-17 over all time periods indicated a random distribution, while the same analysis of segments 10-20 indicated a non-random distribution due to large numbers of worms in segment 20 and to the absence of worms in segment 18. To analyze temporal changes in worm distribution, mice were grouped by time of necropsy as follows: night (1900 and 2300 hr), morning (0300 and 0700 hr), and day (1100 and 1500 hr). During the night and morning, E. caproni was heavily concentrated in segments 10-17 and, during the day, worms were located more posteriorly, with a heavy concentration in the last segment (20).     

A chromosome-based model for estimating the number of conserved segments between pairs of species from comparative genetic maps

Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.     

Ontogenetic variation in fin ray segmentation between latitudinal populations of the medaka, <Emphasis Type="Italic">Oryzias latipes</Emphasis>

Fin rays of ray-finned fishes are composed of multiple bony segments, and each fin ray elongates by adding a new segment to the tip. Therefore, fin ray length is determined by the number of segments and the length of each segment. A comparison of the anal fin rays of a northern and southern wild population of the medaka, Oryzias latipes, revealed that southern fish had more segments per fin ray, resulting in longer anal fins than the northern fish. When fish were reared in a laboratory common environment, segmentation of the fin rays started earlier with respect to body size in the southern fish. In the southern males, moreover, the rate of segment addition accelerated after a certain body size, indicating sexual maturity. These patterns of segment addition during ontogeny were consistent with the patterns of fin ray elongation. Although distal segments tended to be longer, except for the most proximal segment, in both populations, the southern fish had shorter segments than the northern fish at any position on fin rays. These results indicate that the interpopulation variation in fin length is largely due to genetically-based differences in the control of segment addition, and that the length of each segment does not contribute to it. We suspect that fin ray segmentation is regulated by thyroid and sex hormones that differ between populations. We also found that some segments fuse with each other at the base of each fin ray, the functions and mechanisms of which remain unclear.     

Latitudinal cline in segment number in an arthropod species, Strigamia maritima

Arthropods vary more than 30-fold in segment number. The evolutionary origins of differences in segment number among species must ultimately lie in intraspecific variation. Yet paradoxically, in most groups of arthropods, the number of segments is fixed for each species and shows no intra- or interpopulation variation at all. Geophilomorph centipedes are an exception to this general rule, and exhibit intraspecific variation in segment number, with differences between individuals being determined during embryonic development and hence independent of population age structure. Significant differences in segment number between different geographical populations of the same species have been previously reported, but insufficient sampling has been conducted to reveal any particular geographical pattern. Here, we reveal a latitudinal cline in segment number in the geophilomorph species Strigamia maritima: segment number in British populations decreases with distance north. This is the first such cline to be reported for any centipede species; indeed as far as we are aware it is the first such cline reported for any arthropod species. In vertebrates, fish are known to exhibit a latitudinal cline in segment number, but interestingly, this is in the opposite direction; fish add segments with increasing latitude, centipedes subtract them.     

Comparison of sensory structures on the antenna of different species of Philopotamidae (Insecta: Trichoptera)

Structure and distribution of sensilla were studied in sixteen species of the caddisfly family Philopotamidae. Their antennae bear numerous curved trichoid and pseudoplacoid sensilla and fewer coronal, styloconic and chaetoid sensilla on the flagellar segments. The most numerous pseudoplacoid sensilla have non-specific localization. The curved trichoid sensilla form clusters ventrally on each antennal segment. Sensilla belonging to coronal, styloconic and chaetoid types have specific positions. Long grooved trichoid sensilla are located nonspecifically in all the studied species. The average number of sensilla per segment decreases from the proximal to distal part of the flagellum. Scapus and pedicellum are devoid of most types of sensilla, however, they bear the Böhm bristles and long trichoid sensilla. A positive correlation between antenna dimensions and its cuticular structures is found.     

Vertex analysis of Purkinje cell dendritic trees in the cerebellum of the rat

All networks are made up of vertices (points interconnected by segments), which include terminals interconnected by terminal segments, nodes interconnected by link segments and the root point connected to the tree by the root segment. All nodes may be classified into unique types according to the number of terminal and link segments they drain. For example, there are three distinct dichotomous nodes, a 'primary' node draining two terminal segments, a 'secondary' node draining one terminal segment and a link segment, and a 'tertiary' node draining two link segments. The numbers of primary and tertiary nodes approximate to equality in large networks and thus the ratio of primary to secondary nodes defines topology. All higher order nodes ( trichotomous and beyond) may be resolved into dichotomous forms and incorporated into the analysis. Different forms of growth may thus be analysed by comparing the frequency distributions of nodes with those generated by computer simulated growth models. Moreover, all vertices can be ordered so that metrical parameters are easily incorporated and the hierarchical arrangements of vertices of different order discerned. The dendritic trees of 48 Purkinje cells, taken from folia along the primary fissure, were analysed using vertex analysis. The mean number of segments in Purkinje cell trees was 881 +/- 23 (s.e.) and mean total dendritic length 7959 +/- 233 (s.e.) micrometers. Segment lengths were longest over proximal segments but over most of the tree segment lengths were constant at 10 +/- 0.2 (s.e.) micrometers. Vertex, segment and terminal frequency distributions of equivalent orders were all normal with a slight positive skew. Peak frequencies were recorded at the 12th equivalent order. The mean primary/secondary nodal vertex ratio was 0.93 and the proportion of trichotomous branch points in the tree was 5%. Comparison of the frequency distribution of all vertices with computer generated models showed that growth of the Purkinje cell was most closely simulated by a random terminal growth model, incorporating 5% trichotomy , in which the branching of high order terminals was more likely than low order terminals. It was concluded that growth of the Purkinje cell tree could proceed by random terminal branching with growth occurring preferentially over a front composed of terminals that are ascending through a corridor in the molecular layer whose margins are defined by neighbouring trees.     

Quantification of new structural features of coronary plaques by computational post-hoc analysis of virtual histology-intravascular ultrasound images

Cardiovascular disease and complications are often mediated by the development and rupture of atherosclerotic plaques. Plaque composition is a major factor that determines plaque vulnerability. Intravascular ultrasound (IVUS) and spectral analysis of the radio frequency signal provide an in vivo tissue characterisation of atherosclerotic plaques, known as virtual histology (VH–IVUS). In VH–IVUS analysis, four histological tissue components are classified: fibrous, fibro/fatty, necrotic core and calcium. Existing technology determines only the area of each component within the plaque. Quantitative, objective characterisation of other plaque components' patterns within the plaque is lacking. The aim of this study was to determine new compositional and structural indices which indicate spatial distribution, heterogeneity and dispersity of each VH–IVUS-derived component within the plaque area and also with respect to the plaque–lumen border. We developed an automated computational system in Java for the analysis of both single cross-sectional segments and the whole length of the examined plaque (volumetric analysis). The following parameters were computed: the number of different solid segments and the area of the largest solid segment of each component within the plaque, the per cent of the lumen border that is surrounded by each component, the number of different solid segments and the largest area of a solid segment of each component that adjoins the lumen border. Especially components' localisation in relation to the lumen border may significantly influence plaque vulnerability and plaque–stent interaction, which should be investigated in future clinical studies.     

A shared buffer architecture for interactive VOD servers

Video-on-demand (VOD) servers need to be efficiently designed in order to support a large number of users viewing the same or different videos at different rates. While considering a disk-array based VOD server, use of a shared buffer at the server end may be more economical than the sole use of dedicated buffers at each user's end. In this paper, we propose a simple buffer sharing architecture that may be used when disk-array based video servers are used. Our aim is to support the maximum number of users for a given number of video server disks while employing a simple scheme requiring less buffer space. The number of video segment retrievals that can occur within a certain time (the service round) is maximum when the scan disk scheduling algorithm is used. Consequently, we shall assume use of the scan algorithm for disk retrieval. The VOD server has a buffer manager that directs retrieved segments to appropriate buffer locations depending on their release and deadlines. The release and deadlines of segments are such that buffer requirement at the user's set-top box is minimized to two video segments while avoiding video starvation and buffer overflow at the user's end. We propose a novel scheme for the operation of the shared buffer that aims at increasing buffer utilization and decreasing cell loss due to buffer overflow. An ATM based broadband network is assumed and all segments are stored in buffers as fixed length ATM cells. We also use a novel scheme for grouping frames into segments and illustrate its advantages over earlier ones. This revised version was published online in July 2006 with corrections to the Cover Date.     

QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines

Chromosome segment substitution (CSS) lines have the potential for use in QTL fine mapping and map-based cloning. The standard t-test used in the idealized case that each CSS line has a single segment from the donor parent is not suitable for non-idealized CSS lines carrying several substituted segments from the donor parent. In this study, we present a likelihood ratio test based on stepwise regression (RSTEP-LRT) that can be used for QTL mapping in a population consisting of non-idealized CSS lines. Stepwise regression is used to select the most important segments for the trait of interest, and the likelihood ratio test is used to calculate the LOD score of each chromosome segment. This method is statistically equivalent to the standard t-test with idealized CSS lines. To further improve the power of QTL mapping, a method is proposed to decrease multicollinearity among markers (or chromosome segments). QTL mapping with an example CSS population in rice consisting of 65 non-idealized CSS lines and 82 chromosome segments indicated that a total of 18 segments on eight of the 12 rice chromosomes harboured QTLs affecting grain length under the LOD threshold of 2.5. Three major stable QTLs were detected in all eight environments. Some minor QTLs were not detected in all environments, but they could increase or decrease the grain length constantly. These minor genes are also useful in marker-assisted gene pyramiding.     

Computer simulation study of molecular recognition in model DNA microarrays

DNA microarrays have been widely adopted by the scientific community for a variety of applications. To improve the performance of microarrays there is a need for a fundamental understanding of the interplay between the various factors that affect microarray sensitivity and specificity. We use lattice Monte Carlo simulations to study the thermodynamics and kinetics of hybridization of single-stranded target genes in solution with complementary probe DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8-24 segments. The segments on the probe and target are distinct and each segment represents a sequence of nucleotides ( approximately 11 nucleotides). Each probe segment interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how the probe length, temperature, or hybridization energy, and the stretch along the target that the probe segments complement, affect the extent of hybridization. For systems containing single probe and single target molecules, we observe that as the probe length increases, the probability of binding all probe segments to the target decreases, implying that the specificity decreases. We observe that probes 12-16 segments ( approximately 132-176 nucleotides) long gave the highest specificity and sensitivity. This agrees with the experimental results obtained by another research group, who found an optimal probe length of 150 nucleotides. As the hybridization energy increases, the longer probes are able to bind all their segments to the target, thus improving their specificity. The hybridization kinetics reveals that the segments at the ends of the probe are most likely to start the hybridization. The segments toward the center of the probe remain bound to the target for a longer time than the segments at the ends of the probe.     

Three segments from the monkey genome that hybridize to simian virus 40 have common structural elements.

Three cloned segments that hybridize to a region of simian virus 40 (SV40) deoxyribonucleic acid including the origin of replication have been isolated from a monkey genomic library. The primary structure of one segment was previously reported (T. McCutchan and M. Singer, Proc. Natl. Acad. Sci. U.S.A. 78:95-99, 1981). We report here the sequences of the other two segments and a comparison of all three. The SV 40-hybridizing region in each segment is limited to several hundred base pairs. All of the segments contain multiple and disconnected sequences homologous to the region of SV40 directly surrounding the viral replication origin. The number and arrangement of the homologous sequences is different in the three segments. However, the segments have the following features in common: (i) each contains multiple copies of the sequence GGGCGGPuPu, which also appears six times near the origin of SV40; (ii) each contains several strong homologies to the central dyad symmetry of SV40; (iii) each contains a long internal repeat, as does the origin region of SV40. The three SV40-hybridizing segments are members of a larger family of genomic sequences that hybridize well to each other, but not necessarily to SV40.     

The supernumerary segment system of Stethophyma

Three species of the genus Stethophyma have been cytologically examined and all three show variation both for supernumerary heterochromatic segments and for the distribution of standard heterochromatin among the autosomes. The European species, S. grossum, for example, shows considerable interpopulation variation for standard heterochromatin while two of the populations, from Spain and Austria, show supernumerary segment polymorphism. The segments are located interstitially on the S₁₁ chromosome but occupy different positions in the different populations. — In all species, the presence of the extra heterochromatic segments increases the mean chiasma frequency. Moreover, the influence of the segments upon mean chiasma frequency is different in different populations and in different species. In the Spanish population, the increase is both intra- and interchromosomal whereas in Austria the influence of the segment is completely interchromosomal. — In the American species, S. gracile and S. lineatum, where supernumerary heterochromatic segments are carried on both S₁₀ and S₁₁ chromosomes, the effect on chiasma frequency shows a dosage relationship, an increase in the number of segments per individual being correlated with an increase in mean chiasma frequency. It is suggested that the interstitial segments found in all species have originated by direct duplication of chromosome material. By contrast the terminal segments in S. lineatum and S. gracile may be derived by translocation from a B-chromosome since such a chromosome has been found in one individual of the former species. — The variation in segment structure and the distribution of standard heterochromatin, among the European species of S. grossum suggests that these systems have evolved independently in different populations.On educational leave from the Forest Research Laboratory, Fredericton, N. B. Canada.     

Determination of the number of conserved chromosomal segments between species

Genomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 +/- 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of approximately 1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only approximately 0.74 rearrangements per million years.     

Analysis of body segment parameter differences between four human populations and the estimation errors of four popular mathematical models

Calculating the kinetics of motion using inverse or forward dynamics methods requires the use of accurate body segment inertial parameters. The methods available for calculating these body segment parameters (BSPs) have several limitations and a main concern is the applicability of predictive equations to several different populations. This study examined the differences in BSPs between 4 human populations using dual energy x-ray absorptiometry (DEXA), developed linear regression equations to predict mass, center of mass location (CM) and radius of gyration (K) in the frontal plane on 5 body segments and examined the errors produced by using several BSP sources in the literature. Significant population differences were seen in all segments for all populations and all BSPs except hand mass, indicating that population specific BSP predictors are needed. The linear regression equations developed performed best overall when compared to the other sources, yet no one set of predictors performed best for all segments, populations or BSPs. Large errors were seen with all models which were attributed to large individual differences within groups. Equations which account for these differences, including measurements of limb circumferences and breadths may provide better estimations. Geometric models use these parameters, however the models examined in this study did not perform well, possibly due to the assumption of constant density or the use of an overly simple shape. Creating solids which account for density changes or which mimic the mass distribution characteristics of the segment may solve this problem. Otherwise, regression equations specific for populations according to age, gender, race, and morphology may be required to provide accurate estimations of BSPs for use in kinetic equations of motion.     

The structure of interrupted human AC microsatellites

Microsatellite lengths change over evolutionary time through a process of replication slippage. A recently proposed model of this process holds that the expansionary tendencies of slippage mutation are balanced by point mutations breaking longer microsatellites into smaller units and that this process gives rise to the observed frequency distributions of uninterrupted microsatellite lengths. We refer to this as the slippage/point-mutation theory. Here we derive the theory's predictions for interrupted microsatellites comprising regions of perfect repeats, labeled segments, separated by dinucleotide interruptions containing point mutations. These predictions are tested by reference to the frequency distributions of segments of AC microsatellite in the human genome, and several predictions are shown not to be supported by the data, as follows. The estimated slippage rates are relatively low for the first four repeats, and then rise initially linearly with length, in accordance with previous work. However, contrary to expectation and the experimental evidence, the inferred slippage rates decline in segments above 10 repeats. Point mutation rates are also found to be higher within microsatellites than elsewhere. The theory provides an excellent fit to the frequency distribution of peripheral segment lengths but fails to explain why internal segments are shorter. Furthermore, there are fewer microsatellites with many segments than predicted. The frequencies of interrupted microsatellites decline geometrically with microsatellite size measured in number of segments, so that for each additional segment, the number of microsatellites is 33.6% less. Overall we conclude that the detailed structure of interrupted microsatellites cannot be reconciled with the existing slippage/point-mutation theory of microsatellite evolution, and we suggest that microsatellites are stabilized by processes acting on interior rather than on peripheral segments.