Influences of geographic differentiation in the forewing warning signal of the wood tiger moth in Alaska

Aposematic organisms have warning signals advertising their unpalatability to predators, and because signal efficiency is better in higher densities, positive frequency-dependent selection is expected to select against less common signals. The wood tiger moth (Parasemia plantaginis) occurs across the Holarctic and its conspicuous hindwings serve as warning signals to predators. It also has conspicuous black and white forewing patterns that could act as warning signals, or help to hide the moth by preventing predators from seeing the outline of the moth’s body (a strategy known as disruptive coloration). In Alaska, the predominant forewing pattern changes distinctly between the regions around Fairbanks and Anchorage, suggesting local predators may maintain differences if the pattern functions as a warning signal. Alternatively, restricted gene flow along with drift could be responsible. We placed artificial moths with both local dominant and foreign forewing patterns in each of the two regions to test if predators select against the foreign forewing types, which would suggest the warning signal function of forewing patters. We also manipulated the level of disruptiveness in the forewing patterns to see if disruptiveness works in concert with the warning signal. The locally dominant forewing type was better protected in Fairbanks, but not in Anchorage where morphs were attacked equally. Manipulating the level of disruptiveness in the forewing pattern did not influence predation. Population genetic analyses from specimens caught during fieldwork showed the existence of two populations and restricted gene flow. Our results suggest that positive frequency dependent selection may be partially responsible for maintaining local signal differences, although predators seem to avoid both forewing patterns in Anchorage. Restricted gene flow between the two populations could be attributed to a combination of selection against foreign morphs in Fairbanks and physical barriers, which both likely contribute to warning signal differences in Alaska.     

Lithofacies and biostratigraphical correlation of marine Carboniferous rocks in the Tindouf Basin,NW Africa

Spatial and temporal variations of Carboniferous sediment accumulation within the northwestern part of the northern flank of the Tindouf Syncline in Saharan Morocco allowed to distinguish 16 lithofacies types. The predominant sedimentation pattern is cyclic, with the overall succession recording a major regressive trend. Outer platform siliciclastics in the lower part (Tournaisian and Viséan) pass up to middle and inner platform mixed siliciclastic and carbonate sediments (late Viséan–Serpukhovian) and finally to continental sandstones in the Bashkirian capping the marine carbonate sedimentation. The lack of similarities in a correlation with southern outcrops in the Tindouf Syncline suggests tectonically controlled sedimentation. The upper Tournaisian to lower Bashkirian succession records the incipient uplift of the Anti-Atlas Mountains, changing the paleogeography and, therefore, affecting the paleoecologic conditions, as well as the sedimentary environments in the Tindouf Basin. It is suggested that from the Serpukhovian onwards, much of the Anti-Atlas was uplifted, leading to subaerial conditions, while during the late Viséan, only a few small inliers had emerged. Although the number of Proterozoic emergent inliers of the Anti-Atlas is unknown, during the late Viséan, the Anti-Atlas Mountain belt is regarded as an emerging structure, with a distinct influence on the paleobiogeography of the region.     

Prominent spermoderm patterns of Poaceae

Scanning electron microscopy studies of 60 genera and 118 species of the Poaceae revealed prominent spermoderm patterns. The most common patterns observed (with percent occurrence) were simple reticulate with straight walls (48.3%), simple reticulate with wavy walls (14.4%), and verrucate without pubescence (13.6%). No other pattern occurred in more than 10% of the species observed. Some genera possess common spermoderm patterns among species while others do not.     

SmartJoin: a network-aware multiway join for MapReduce

MapReduce is an effective tool for processing large amounts of data in parallel using a cluster of processors or computers. One common data processing task is the join operation, which combines two or more datasets based on values common to each. In this paper, we present a network aware multi-way join for MapReduce (SmartJoin) that improves performance and considers network traffic when redistributing workload amongst reducers. SmartJoin achieves this by dynamically redistributing tuples directly between reducers with an intelligent network aware algorithm. We show that our presented technique has significant potential to minimize the time required to join multiple datasets. In our evaluation, we show that SmartJoin has up to 39 % improvement compared to the non-redistribution method, a 26.8 % improvement over random redistribution and 27.6 % improvement over worst join redistribution.     

A dynamic block device reconfiguration algorithm in virtual MapReduce cluster

With the advances of cloud computing and virtualization technologies, running MapReduce applications over clouds has been attracting more and more attention in recent years. However, as a fundamental problem, the performance of MapReduce applications can sometimes be severely degraded due to the overheads from I/O virtualization and resource competitions among virtual machines. In this paper, we propose a dynamic block device reconfiguration algorithm in virtual MapReduce clusters, which reduces the data transfer time between virtual machines and thereby improving the performance of MapReduce applications on top of the clouds. The proposed algorithm utilizes a block device reconfiguration scheme, where a block device attached to a virtual machine can be dynamically detached and reattached to other virtual machines at runtime. This scheme allows us to move files easily across different virtual machines without any network transfers between virtual machines. This algorithm is also dynamic in a sense that it estimates the total data transfer times between virtual machines using multiple regression analysis based on CPU utilization and data size, and adaptively determines a least-cost data transfer path between a mapper virtual machine and a reducer virtual machine. We have implemented our algorithm in Hadoop MapReduce. The benchmarking results showed that the overheads incurred by transferring data from mapper virtual machines to reducer virtual machines are minimized and the execution times of MapReduce applications are shortened up to 14 %.     

Mitochondrial DNA haplogroups and homogeneity in the Korean population

Mitochondrial DNA (mtDNA) haplogroup data provide valuable information for inferring patterns of variation and population structure of maternal lineages. In this study, we analyzed the distribution of mtDNA haplogroup variation using a 20-plex SNaPshot assay for determination of the major East Asian haplogroups to evaluate the possible genetic structure and differentiation from 708 unrelated individuals residing in six major provinces in Korea. The most common mtDNA haplogroups were found to be D4 and B4, followed by A, D4a, and M7, which are prevalent in East Asian populations. All provinces exhibited high haplogroup diversities, ranging from 0.8957 in Jeju Island to 0.9284 in Gyeongsang. Pair-wise F _ST distances and AMOVA of the studied Korean provinces reflected no maternal subpopulation heterogeneity present within the population group, except for Jeju Island, showing small, but statistically significant differences between the populations (p < 0.01). This result indicates that the Jeju Island may point to the need for creating a local mtDNA database, to avoid bias in forensic parameters estimates caused by genetic heterogeneity of the population. However, since there is no geographic pattern to suggest this result represents any population heterogeneity on a peninsular level in Korea, the present data could be useful in serving as a basis for comprehensive Korean population and forensic mtDNA database.     

FastMPJ: a scalable and efficient Java message-passing library

The performance and scalability of communications are key for high performance computing (HPC) applications in the current multi-core era. Despite the significant benefits (e.g., productivity, portability, multithreading) of Java for parallel programming, its poor communications support has hindered its adoption in the HPC community. This paper presents FastMPJ, an efficient message-passing in Java (MPJ) library, boosting Java for HPC by: (1) providing high-performance shared memory communications using Java threads; (2) taking full advantage of high-speed cluster networks (e.g., InfiniBand) to provide low-latency and high bandwidth communications; (3) including a scalable collective library with topology aware primitives, automatically selected at runtime; (4) avoiding Java data buffering overheads through zero-copy protocols; and (5) implementing the most widely extended MPI-like Java bindings for a highly productive development. The comprehensive performance evaluation on representative testbeds (InfiniBand, 10 Gigabit Ethernet, Myrinet, and shared memory systems) has shown that FastMPJ communication primitives rival native MPI implementations, significantly improving the efficiency and scalability of Java HPC parallel applications.     

Temporal pattern discrimination of impulse sequences in the computer-simulated nerve cells

This paper deals with some properties of temporal pattern discrimination performed by single digital-computer simulated synaptic cells. To clarify these properties, the Shannon's entropy method which is a basic notion in the information theory and a fundamental approach for the design of pattern classification system was applied to input-output relations of the digital computer simulated synaptic cells. We used the average mutual information per symbol as a measure for the temporal pattern sensitivity of the nerve cells, and the average response entropy per symbol as a measure for the frequency transfer characteristics. To use these measures, the probability of a post-synaptic spike as a function of the recent history of pre-synaptic intervals was examined in detail. As the results of such application, it was found that the EPSP size is closely related to the pattern of impulse sequences of the input, and the average mutual information per symbol for EPSP size is given by a bimodal curve with two maximum values. One is a small EPSP size and the other is a large EPSP size. In two maximum points, the structure of the temporal pattern discrimination reverses each other. In addition, the relation between the mean frequency, or the form of impulse sequences of the input, and the average mutual information per symbol has been examined. The EPSP size at one maximum point of average mutual information is in inverse proportion to the magnitude of input mean frequency which relates to the convergence number of input terminal, while that at the other maximum point is proportional to that of the mean frequency. Moreover, the temporal pattern discrimination is affected remarkably by whether successive interspike intervals of the input are independent or not in the statistical sense. Computer experiments were performed by the semi-Markov processes with three typical types of transition matrixes and these shuffling processes. The average mutual informations in the cases of these semi-Markov processes are in contrast to those of the shuffling processes which provide a control case. The temporal structure of successive interspike intervals of the input is thus a significant factor in pattern discrimination at synaptic level.     

The evolutionary pattern of aromatic amino acid biosynthesis and the emerging phylogeny of pseudomonad bacteria

Pseudomonad bacterial are a phylogenetically diverse assemblage of species named within contemporary genera that includePseudomonas, Xanthomonas andAlcaligenes. Thus far, five distinct rRNA homology groups (Groups I through V) have been established by oligonucleotide cataloging and by rRNA/DNA hybridization. A pattern of enzymic features of aromatic amino acid biosynthesis (enzymological patterning) is conserved at the level of rRNA homology, five distinct and unambiguous patterns therefore existing in correspondence with the rRNA homology groups. We sorted 87 pseudomonad strains into Groups (and Subgroups) by aromatic pathway patterning. The reliability of this methodology was tested in a blind study using coded cultures of diverse pseudomonad organisms provided by American Type Culture Collection. Fourteen of 14 correct assignments were made at the Group level (the level of rRNA homology), and 12 of 14 correct assignments were made at the finer-tuned Subgroup levels. Many strains of unknown rRNA-homology affiliation had been placed into tentative rRNA groupings based upon enzymological patterning. Positive confirmation of such strains as members of the predicted rRNA homology groups was demonstrated by DNA/rRNA hybridization in nearly every case. It seems clear that the combination of these molecular approaches will make it feasible to deduce the evolution of biochemical-pathway construction and regulation in parallel with the emerging phylogenies of microbes housing these pathways.     

Polymorphism in B-DNA: X-ray diffraction studies on Li-DNA fibres

From X-ray diffraction studies it is generally believed that B-DNA has the structural parameters n = 10 and h = 3.4 Å. However, for the first time we report that polymorphism in the B-form can be observed in DNA fibres. This was achieved by the precise control of salt and humidity in fibres and by the application of the precession method of X-ray diffraction to DNA fibres. The significant result obtained is that n = 10 is not observed for crystalline fibre patterns. In fact, n = 10 and h = 3.4 Å are not found to occur simultaneously. Instead, a range of values, n = 9.6–10.0 and h = 3.35 Å–3.41 Å is observed.     

Genetic structure and inter-generic relationship of closed colony of laboratory rodents based on RAPD markers

Molecular genetic analysis was performed using random amplified polymorphic DNA (RAPD) on three commonly used laboratory bred rodent genera viz. mouse (Mus musculus), rat (Rattus norvegicus) and guinea pig (Cavia porcellus) as sampled from the breeding colony maintained at the Animal Facility, CSIR-Indian Institute of Toxicology Research, Lucknow. In this study, 60 samples, 20 from each genus, were analyzed for evaluation of genetic structure of rodent stocks based on polymorphic bands using RAPD markers. Thirty five random primers were assessed for RAPD analysis. Out of 35, only 20 primers generated a total of 56.88 % polymorphic bands among mice, rats and guinea pigs. The results revealed significantly variant and distinct fingerprint patterns specific to each of the genus. Within-genera analysis, the highest (89.0 %) amount of genetic homogeneity was observed in mice samples and the least (79.3 %) were observed in guinea pig samples. The amount of genetic homogeneity was observed very high within all genera. The average genetic diversity index observed was low (0.045) for mice and high (0.094) for guinea pigs. The inter-generic distances were maximum (0.8775) between mice and guinea pigs; and the minimum (0.5143) between rats and mice. The study proved that the RAPD markers are useful as genetic markers for assessment of genetic structure as well as inter-generic variability assessments.     

Neutralization of bacterial viruses by antibodies of young animals

The cofactor activity of complement of precolostral newborn pig serum was compared with the haemolytic and bactericidal activity. Using current decomplementation treatment it was found that all three types of activity are destroyed in parallel i.e. haemolytic, bactericidal and cofactor (heat inactivation, EDTA, ammonia, trypsin, adsorption to zymosan or immune precipitate). In an ultracentrifugation analysis the haemolytic, bactericidal and cofactor activities showed the same sedimentation pattern. Using gel filtration on a Sephadex G 200 column, the cofactor activity was found in the fraction which contained all basic complement components. On the basis of these results it can be concluded that the complement of piglet serum acts as a factor which potentiates the neutralization of bacteriophage by the sera of the newborn.     

Peroxidase,polyphenol oxidase and catalase isoenzymes during germination and early plant development of tall and dwarf wheats (Triticum aestivum L.)

Isoenzyme pattern of peroxidase, polyphenol oxidase and catalase at different intervals during germination and in different plant parts during early development of ‘C-306’ and ‘Hira’ cultivars, representing tall and dwarf wheats, respectively were investigated. The number of isoenzymic components of the three enzymes increased progressively with the concomitant increase in the stage of germination. The isoenzymic patterns, in general, were more clear and better developed during the later stages of germination. Different tissues or organs of the wheat plant possessed specific isoenzymic pattern of these enzymes. Differences between cultivars were observed both in the number and relative intensity of the various isoenzymic fractions.     

Does light spectral quality affect survival and regeneration of potato (Solanum tuberosum L.) shoot tips after cryopreservation?

Cryopreservation, the storage of germplasm at ultra-low temperature is the most reliable tool for long-term preservation of plant genetic resources. Cryopreservation techniques are widely applied but the effect of light spectra on plant recovery after cryopreservation is largely unknown. Therefore, we investigated the effect of different light spectral qualities on survival and regeneration of shoot tips of potato (Solanum tuberosum L.) cultivars Agrie Dzeltenie, Maret, Bintje, Désirée and Anti cryopreserved by the DMSO-droplet method. Prior to cryopreservation, the plants were stored under cool white fluorescent light (CW). Post-cryopreservation, the plants were allowed to regenerate under six different light qualities: CW, warm white light (HQI), blue LEDs (B), red LEDs (R), red with 10 % of blue (RB) and RBF - red with 10 % of blue with addition of 20 % of far-red LEDs. The light spectral quality had a significant effect on the survival and regeneration of potato shoot tips after cryopreservation. The combination of red light with 10 % of blue (RB) doubled the regeneration percentage of all cultivars, whereas red light (R) was not suitable for regeneration after cryopreservation. Specifically, the regeneration percentages were increased in RB compared to CW from 25.5 to 52.6 % for ‘Agrie Dzeltenie’, 25.0–43.6 % for ‘Maret’, 8.1–26.1 % for ‘Bintje’, 0.0–17.1 % for ‘Anti’ and 18.2–36.6 % for ‘Désirée‘. Therefore, the modification of light spectra during the recovery phase is a promising tool for increasing the regeneration of potato shoot tips after cryopreservation.