Urine marking and social dominance in male house mice (Mus musculus domesticus)

House mice use urine marking for a variety of forms of social communication. Urine marking varies with dominance status; socially dominant male house mice urine mark more than those that are socially subordinate. Experiment I was designed to confirm this previous finding. Experiment II was designed to test whether urine marking, measured prior to testing males for aggression, could be used to predict social dominance. Mice were tested for urine marking in 20 cmx40 cm rectangular cages with filter paper below the wire mesh bottom of the cage. In Experiment I, groups of four males were tested in a round robin design to assess social dominance and were then placed individually in urine marking cages. Social dominance was a significant predictor of the number of 1 cm squares that contained urine marks, both with regard to interior squares and for perimeter squares in the test cage. In Experiment II, groups of four males were first tested individually in urine marking cages and then used for round robin aggressive encounters to assess social dominance. The number of interior squares with urine marks, and, to a lesser extent, the number of perimeter squares with urine marks, were both significant predictors of aggression scores and social dominance status. Being able to judge social dominance without having the mice encounter each other could be a valuable tool for future work; confounding effects on such parameters as hormone levels could be avoided while obtaining an estimate of male social dominance status.     

Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm

We have parallelized the FASTA algorithm for biological sequencecomparison using Linda, a machine-independent parallel programminglanguage. The resulting parallel program runs on a variety ofdifferent parallel machines. A straightforward parallelizationstrategy works well if the amount of computation to be doneis relatively large. When the amount of computation is reduced,however, disk I/O becomes a bottleneck which may prevent additionalspeed-up as the number of processors is increased. The paperdescribes the parallelization of FASTA, and uses FASTA to illustratethe I/O bottleneck problem that may arise when performing paralleldatabase search with a fast sequence comparison algorithm. Thepaper also describes several program design strategies thatcan help with this problem. The paper discusses how this bottleneckis an example of a general problem that may occur when parallelizing,or otherwise speeding up, a time-consuming computation. Received on July 25, 1990; accepted on October 15, 1990     

He—Ne激光对家蚕诱变效应的研究

采用一定剂量的ＨｅＮｅ激光辐照家蚕蛹,在子代与对照相比较,出现熟性、茧形、斑纹等多种变异,利用ＰＡＧＥ,进行血液蛋白质电泳分析结果,也产生谱带数目及活性的变化,首次证明ＨｅＮｅ激光对家蚕具有一定的诱变效应。     

Improved methods for color‐marking hummingbirds

ABSTRACT Individual color‐marking is an essential tool for studying the behavior of free‐living birds. Hummingbirds represent a particular challenge for traditional avian color‐marking techniques because of their small size and short tarsi. Although several techniques have been successfully used, the retention time of color‐markers and their safety and ease of construction could be improved. I developed two new color‐marking techniques for marking Little Hermits (Phaethornis longuemareus): (1) a plastic back tag constructed by fusing colored beads, and (2) a leg tag attached to a metal band fitted around the tarsus. Both tag designs were visible in field conditions, and neither appeared to adversely affect behavior. Both back and leg tags had high retention rates within seasons, but back tags had a poor retention rate between years. Although these marking techniques were designed for use on one species of hummingbird, they would likely also be useful with other species of hummingbirds.     

biobambam: tools for read pair collation based algorithms on BAM files

Background

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs.

Results

In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package.

Conclusions

In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

     

A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection

Separation of complex mixtures of proteins by two-dimensional gel electrophoresis (2-DE) is a fundamental component of current proteomic technology. Quantitative analysis of the images generated by digitization of such gels is critical for the identification of alterations in protein expression within a given biological system. Despite the availability of several commercially available software packages designed for this purpose, image analysis is extremely resource intensive, subjective and remains a major bottleneck. In addition to reducing throughput, the requirement for manual intervention results in the introduction of operator subjectivity, which can limit the statistical significance of the numerical data generated. A key requirement of image analysis is the accurate definition of protein spot boundaries using a suitable method of image segmentation. We describe a method of spot detection applicable to 2-DE image files using a segmentation method involving pixel value collection via serial analysis of the image through its range of density levels. This algorithm is reproducible, sensitive, accurate and primarily designed to be automatic, removing operator subjectivity. Furthermore, it is believed that this method may offer the potential for improved spot detection over currently available software.     

Parallel Clustering Algorithm for Large-Scale Biological Data Sets

Backgrounds

Recent explosion of biological data brings a great challenge for the traditional clustering algorithms. With increasing scale of data sets, much larger memory and longer runtime are required for the cluster identification problems. The affinity propagation algorithm outperforms many other classical clustering algorithms and is widely applied into the biological researches. However, the time and space complexity become a great bottleneck when handling the large-scale data sets. Moreover, the similarity matrix, whose constructing procedure takes long runtime, is required before running the affinity propagation algorithm, since the algorithm clusters data sets based on the similarities between data pairs.

Methods

Two types of parallel architectures are proposed in this paper to accelerate the similarity matrix constructing procedure and the affinity propagation algorithm. The memory-shared architecture is used to construct the similarity matrix, and the distributed system is taken for the affinity propagation algorithm, because of its large memory size and great computing capacity. An appropriate way of data partition and reduction is designed in our method, in order to minimize the global communication cost among processes.

Result

A speedup of 100 is gained with 128 cores. The runtime is reduced from serval hours to a few seconds, which indicates that parallel algorithm is capable of handling large-scale data sets effectively. The parallel affinity propagation also achieves a good performance when clustering large-scale gene data (microarray) and detecting families in large protein superfamilies.     

Experimental optimization of protein refolding with a genetic algorithm

Refolding of proteins from solubilized inclusion bodies still represents a major challenge for many recombinantly expressed proteins and often constitutes a major bottleneck. As in vitro refolding is a complex reaction with a variety of critical parameters, suitable refolding conditions are typically derived empirically in extensive screening experiments. Here, we introduce a new strategy that combines screening and optimization of refolding yields with a genetic algorithm (GA). The experimental setup was designed to achieve a robust and universal method that should allow optimizing the folding of a variety of proteins with the same routine procedure guided by the GA. In the screen, we incorporated a large number of common refolding additives and conditions. Using this design, the refolding of four structurally and functionally different model proteins was optimized experimentally, achieving 74–100% refolding yield for all of them. Interestingly, our results show that this new strategy provides optimum conditions not only for refolding but also for the activity of the native enzyme. It is designed to be generally applicable and seems to be eligible for all enzymes.     

Online control of evaluation algorithms of the image applied to identification of deglutition function]

Comprehensive software and hardware have been developed for the processing of biosignals. Such automatic signal processing, however not only has advantages, but also drawbacks. The question as to the reliability of the evaluation algorithm arises when the signal is modified, in the presence of interindividual differences, and in particular when noise is superimposed. This is of great interest for long-term recording when the original signal can no longer be inspected visually. The aim of our work was to display the signals on the screen of a monitor simultaneously with lines marking the points (start, end, extreme value, etc.) processed by the specific signal processing algorithm. The program package permits the on-line recording and monitoring of signals, the parallel processing and marking of detected events on the monitor, as well as storage of the parameters extracted. It is a very effective tool for developing, improving and monitoring of algorithms and their efficiency for signal processing.     

鲈鲤早期鱼苗的耳石标记研究

为研究鲈鲤早期鱼苗耳石标记的可行性,先采用高温水(20.8±0.3)℃和低温水(10.8±1.2)℃交替饲养对20日龄鲈鲤进行热标记,然后将经热标记的35和45日龄鲈鲤浸泡在50—200 mg/L的茜素络合物(AC)或茜素红S(ARS)溶液中进行荧光标记。热标记的耳石生长轮清晰可见,明显区别于其他轮纹,微耳石热标记轮轮纹宽度(IW)和高温期持续时间(T)的线性回归方程为IW=0.16462+0.24762T。经荧光物质浸泡后鲈鲤耳石在绿光下均能检测到橘红色标记; AC标记质量受溶液浓度影响显著(P<0.05),受全长的影响不显著(P>0.05),微耳石、矢耳石和星耳石间的标记质量差异显著(P<0.05); ARS标记质量受全长和溶液浓度影响不显著(P>0.05),微耳石、矢耳石和星耳石间的标记质量差异显著(P<0.05)。研究结果表明,耳石热标记、荧光标记及两者结合使用均可用于大规模标记鲈鲤早期鱼苗。     

Do bottlenecks increase additive genetic variance?

Because of anthropogenic factors many populations have been at least temporarily reduced to a very small population size. Such reductions could potentially decrease genetic variation and increase the probability of extinction. Analysis of molecular markers has shown a decrease in genetic variation but in many cases this has not reduced the ability of the population to recover from the bottleneck. This apparent paradox is resolved by a consideration of how population bottlenecks can affect additive genetic variance, the relevant measure of ability to respond to selective factors. A bottleneck has the potential to increase additive genetic variance in a population. This may result in an increase in fitness, particularly in populations of conservation concern that are small and lack genetic variation. Here we present a meta-analysis of experimental tests of this prediction using models designed to fit data that is strictly additive and data that has non-additive components. This analysis shows that additive genetic variance in a dataset dominated by morphological traits increases, on average, after a bottleneck event when the inbreeding coefficient is less than 0.3, but neither of the theoretical models alone can adequately explain this result. Because of our inability at present to predict the results of a population bottleneck in a specific case and the probability of extinction associated with small population size we caution against using bottlenecks to increase genetic variance, and thus the fitness, of endangered populations.     

Spatial patterns of scent marking in wild moustached tamarins, Saguinus mystax: no evidence for a territorial function

I investigated whether scent marking has a territorial function in wild moustached tamarins. I examined the spatial distribution of scent marking within the home ranges of four groups of this neotropical primate and tested predictions from Gorman & Mills' (1984, Journal of Zoology,202, 535-547) model for border and 'hinterland' marking. Although home ranges were economically defensible, no evidence was found for increased marking along the territorial boundary or in areas of home range overlap, but there was also no evidence for hinterland marking. Observed distributions of scent marking in exclusively used and overlapping areas of the home range did not deviate from distributions that would be expected if scent marking occurred at random (expectation based both on size of area and on frequency of quadrat occupation), and there was a strong correlation between frequency of quadrat occupation and frequency of scent marking per quadrat. These results indicate that scent marking has no territorial function in moustached tamarins. This is in line with mainly qualitative findings from the majority of other studies on wild marmosets and tamarins. These and other findings on scent marking in moustached tamarins suggest that this behaviour functions mainly in intersexual communication. Copyright 2000 The Association for the Study of Animal Behaviour.     

Scent Marking in Voles: A Reassessment of Over Marking, Counter Marking, and Self-Advertisement

We conducted a series of experiments to discern among the counter-marking, over-marking, and self-advertisement hypotheses for secondary marking in male prairie voles, Microtus ochrogaster , and meadow voles, M. pennsylvanicus . Secondary scent marks (those placed in an area that has already been marked by a conspecific) were not significantly greater than initial marks placed on clean substrate (a substrate without any previous scent marks) for either species and thus did not support a counter-marking hypothesis. Similarly, overlapping of initial scent marks with secondary marks occurred less often than expected by chance and did not support an over-marking hypothesis. Secondary marks tended to avoid overlap with scent marks previously deposited by a potential competitor. Our results suggest that secondary scent marking functions to self-advertise by maximizing individual identity and avoiding masking or blending with previous donors. Future studies on secondary marking should be designed to quantify the observed and expected frequency and placement of original and secondary marks to discern among alternative hypotheses for the adaptive significance of secondary marking.     

Tagging the next generation: validation of trans-generational chemical tagging for an endangered fish

In this study we validated marking offspring through peritoneal injection of ripe females using two concentrations of strontium (strontium chloride hexahydrate). Larvae from treatments were monitored for condition morphometrics and tested for chemical mark incorporation in their otoliths via laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) to quantify the strontium concentration (Sr/Ca) and laser ablation multi-collector inductively coupled plasma mass spectrometry (LA-MC-ICPMS) to measure the strontium isotope ratios (⁸⁷Sr:⁸⁶Sr) of otoliths. Otolith strontium concentrations and strontium isotopes ratios were elevated in the high-concentration treatment, while the low-concentration and control treatments were not significantly different from each other. Larval size and eye diameter at hatch were similar among treatments; however, yolk and oil globule diameters were significantly reduced in the high-concentration treatment. Moreover, growth rates after 60?days post-hatch were significantly reduced in the high-concentration treatment relative to the low-concentration and control treatments, suggesting trans-generational tagging can have deleterious effects on offspring. Our study provides evidence for the efficacy of artificially marking offspring via injection of strontium into ripe females and could provide new tools for managing endangered fish populations; however, careful consideration of chemical concentrations and dosages may be required prior to its application in a fisheries management experiment.     

Ultrastructural localization of Kunitz inhibitor on thin sections of Glycine max (soybean) cv. Maple Arrow by the gold method

The soybean trypsin inhibitor (SBTI, Kunitz type) was localized by immunofluorescence and, at the ultrastructural level, by the protein A gold method on thin sections of Glycine max (soybean) cv. Maple Arrow. SBTI was localized in cell walls, protein bodies, the cytoplasm between the lipid-containing spherosomes, and the nucleus of the cotyledon and embryonic axis. In the nucleus, SBTI was present in the chromatin deposit and the nucleolus. The intensity of marking by the gold method decreased in the cell wall from the center of the cotyledon to the periphery. In four-days-old seedlings marking intensity of cell wall was much reduced. No SBTI could be detected in the hypocotyl. In two lines lacking soybean agglutinin (Norredo, T-102) the location of SBTI was similar to that observed in Maple Arrow. In P.I. 196168, a line lacking SBTI, marking intensity of the organelles was reduced to a very low level. Although this study was not designed to discern the cellular function of SBTI, if any, it may establish criteria consistent with its role in soybean.     

Genetic analysis of a documented population bottleneck: introduced Bennett's wallabies (Macropus rufogriseus rufogriseus) in New Zealand

Few bottlenecks of wild populations are sufficiently well-documented to constitute models for testing theories about the impact of bottlenecks on genetic variation, and subsequent population persistence. Relevant details of the Bennett's wallaby (Macropus rufogriseus rufogriseus) introduction into New Zealand were recorded (founder number, source and approximate bottleneck duration) and suggest this may provide a rare opportunity to examine the efficacy of tests designed to detect recent bottlenecks in wild populations. We first assessed the accuracy of historic accounts of the introduction using genetic diversity detected in mitochondrial DNA (mtDNA) and at five microsatellite loci. Phylogenetic analyses of mtDNA D-loop sequence haplotypes were consistent with the reported origin of the founders as Tasmania, rather than one of the Bass Strait islands in which Bennett's wallabies are also found. Microsatellite allele frequencies from the Tasmanian source population were then used to seed bottleneck simulations encompassing varying sizes and numbers of generations, in order to assess the severity of bottleneck consistent with diversity observed in the New Zealand population. The results suggested that the founder number was unlikely to have been as small as the three animals suggested by the account of the introduction. Nonetheless, the bottleneck was probably severe; in the range of three to five pairs of wallabies for one to three generations. It resulted in significantly reduced levels of allelic diversity and heterozygosity relative to the source population. This bottleneck is only detectable under the infinite allele model (IAM) and not under the stepwise mutation model (SMM) or the two-phase model (TPM), and possible explanations for this are discussed.     

Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics

Large sets of bioinformatical data provide a challenge in time consumption while solving the cluster identification problem, and that is why a parallel algorithm is so needed for identifying dense clusters in a noisy background. Our algorithm works on a graph representation of the data set to be analyzed. It identifies clusters through the identification of densely intraconnected subgraphs. We have employed a minimum spanning tree (MST) representation of the graph and solve the cluster identification problem using this representation. The computational bottleneck of our algorithm is the construction of an MST of a graph, for which a parallel algorithm is employed. Our high-level strategy for the parallel MST construction algorithm is to first partition the graph, then construct MSTs for the partitioned subgraphs and auxiliary bipartite graphs based on the subgraphs, and finally merge these MSTs to derive an MST of the original graph. The computational results indicate that when running on 150 CPUs, our algorithm can solve a cluster identification problem on a data set with 1,000,000 data points almost 100 times faster than on single CPU, indicating that this program is capable of handling very large data clustering problems in an efficient manner. We have implemented the clustering algorithm as the software CLUMP.     

Automated detection and mapping of electrical activation when electrogram morphology is complex

BackgroundMapping of cardiac electrical activity can be difficult when electrogram morphology is complex. Complex morphology (multiple and changing deflections) causes activation maps to vary when constructed by different analysts, particularly at areas with spatially varying conduction pattern. An algorithm was developed to automatically detect electrogram activation time which is robust to complex morphology.MethodElectrograms, many of which were complex, were collected from 320 canine epicardial border zone sites in five experiments. A library of electrogram activation times were manually marked a priori by two expert analysts. Then an algorithm which combined correlation and error functions was used to compare each input electrogram to library electrogram patterns. The closest match of input to library electrogram was used to estimate activation time. Once activation times at 320 sites were determined, activation maps were automatically constructed on a computerized grid. The algorithm was validated by comparison with activation times determined by the analysts.ResultsThe mean difference between manual and automated marking of activation time in electrograms acquired during reentrant ventricular tachycardia was 2.1 ± 3.9 ms. The mean sensitivity and positive predictive value were 95.9% and 83.8% respectively. The computer-automated marking process was completed within a few seconds and was robust to fractionated electrograms. Measurement error was mostly attributable to 60 Hz noise, which can be rectified with filtering.ConclusionsThe automated algorithm is useful for rapid and accurate automatic marking of multichannel electrograms, some of which may be fractionated, as well as for real-time display of activation maps in clinical electrophysiology or research studies.     

Investigation of the performance of fermentation processes using a mathematical model including effects of metabolic bottleneck and toxic product on cells

A number of recent research studies have focused on theoretical and experimental investigation of a bottleneck in a metabolic reaction network. However, there is no study on how the bottleneck affects the performance of a fermentation process when a product is highly toxic and remarkably influences the growth and death of cells. The present work therefore studies the effect of bottleneck on product concentrations under different product toxicity conditions. A generalized bottleneck model in a fed-batch fermentation is constructed including both the bottleneck and the product influences on cell growth and death. The simulation result reveals that when the toxic product strongly influences the cell growth and death, the final product concentration is hardly changed even if the bottleneck is removed, whereas it is markedly changed by the degree of product toxicity. The performance of an ethanol fermentation process is also discussed as a case example to validate this result. In conclusion, when the product is highly toxic, one cannot expect a significant increase in the final product concentration even if removing the bottleneck; rather, it may be more effective to somehow protect the cells so that they can continuously produce the product.     

Chimeric Cellulase Matrix for Investigating Intramolecular Synergism between Non-hydrolytic Disruptive Functions of Carbohydrate-binding Modules and Catalytic Hydrolysis

The conversion of renewable cellulosic biomass is of considerable interest for the production of biofuels and materials. The bottleneck in the efficient conversion is the compactness and resistance of crystalline cellulose. Carbohydrate-binding modules (CBMs), which disrupt crystalline cellulose via non-hydrolytic mechanisms, are expected to overcome this bottleneck. However, the lack of convenient methods for quantitative analysis of the disruptive functions of CBMs have hindered systematic studies and molecular modifications. Here we established a practical and systematic platform for quantifying and comparing the non-hydrolytic disruptive activities of CBMs via the synergism of CBMs and a catalytic module within designed chimeric cellulase molecules. Bioinformatics and computational biology were also used to provide a deeper understanding. A convenient vector was constructed to serve as a cellulase matrix into which heterologous CBM sequences can be easily inserted. The resulting chimeric cellulases were suitable for studying disruptive functions, and their activities quantitatively reflected the disruptive functions of CBMs on crystalline cellulose. In addition, this cellulase matrix can be used to construct novel chimeric cellulases with high hydrolytic activities toward crystalline cellulose.