Students' cellular and molecular explanations of genetic phenomena

Genetic concepts are assigned to three principal levels of organisation: macroscopic level, microscopic level, and submicroscopic level. In order to probe Israeli students' understanding at each level, and to gain a sense of their ability to connect ideas and concepts across different levels, we asked three different types of question. Two of the question types ask students to make a bridge between levels by asking them to explain a phenomenon at one level using concepts and processes from a different level. For example, to explain the appearance of phenotypic traits (macroscopic level) using concepts like genes or chromosomes (microscopic level). One question dealt with the molecular level only. We investigated three populations: 9^th graders, 12^th graders, and pre-service teachers. Based on our findings we suggest improvements both in terms of teaching methods and curriculum content.     

Parental effects of conditional mutations and their explanations

A study of the properties of conditional dominant and recessive lethals in Drosophila melanogaster has demonstrated parental effects in the inheritance and manifestation of these mutations. Maternal and paternal effects are present when conditional mutations interact with (1) one another, (2) the Y chromosome, or (3) chromosomal rearrangements, as well as (4) when the visual expression of a conditional mutation is inherited or (5) during the formation of morphoses (monstrosities) in mutant offspring. The maternal and paternal effects do not exclude one another: the same mutation can display both patterns. The characters manifesting themselves at late developmental stages (morphoses) are inherited according to a parental effect pattern. A general concept of the parental effect is proposed and its types are classified.     

Global environmental impacts: data sources and methodological choices for calculating normalization factors for LCA

The International Journal of Life Cycle Assessment - Characterizing environmental impacts at the global scale is crucial to define references against which compare the environmental profile of...     

concatenator: sequence data matrices handling made easy

concatenator is a simple and user-friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice-versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.     

A suite of Perl modules for handling microarray data

We describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. AVAILABILITY: Software is available at http://sourceforge.net/projects/perlmat     

An expectation-maximization-likelihood-ratio test for handling missing data: application in experimental crosses

The mapping of quantitative trait loci (QTL) is an important research question in animal and human studies. Missing data are common in such study settings, and ignoring such missing data may result in biased estimates of the genotypic effect and thus may eventually lead to errant results and incorrect inferences. In this article, we developed an expectation-maximization (EM)-likelihood-ratio test (LRT) in QTL mapping. Simulation studies based on two different types of phylogenetic models revealed that the EM-LRT, a statistical technique that uses EM-based parameter estimates in the presence of missing data, offers a greater statistical power compared with the ordinary analysis-of-variance (ANOVA)-based test, which discards incomplete data. We applied both the EM-LRT and the ANOVA-based test in a real data set collected from F2 intercross studies of inbred mouse strains. It was found that the EM-LRT makes an optimal use of the observed data and its advantages over the ANOVA F-test are more pronounced when more missing data are present. The EM-LRT method may have important implications in QTL mapping in experimental crosses.     

Microarrays: handling the deluge of data and extracting reliable information

Application of powerful, high-throughput genomics technologies is becoming more common and these technologies are evolving at a rapid pace. Genomics facilities are being established in major research institutions to produce inexpensive, customized cDNA microarrays that are accessible to researchers in a broad range of fields. These high-throughput platforms have generated a massive onslaught of data, which threatens to overwhelm researchers. Although microarrays show great promise, the technology has not matured to the point of consistently generating robust and reliable data when used in the average laboratory. This article addresses several aspects related to the handling of the deluge of microarray data and extracting reliable information from these data. We review the essential elements of data acquisition, data processing and data analysis, and briefly discuss issues related to the quality, validation and storage of data. Our goal is to point out some of the problems that must be overcome before this promising technology can achieve its full potential.     

Colour choices of naive bumble bees and their implications for colour perception

The innate preferences of inexperienced bumble bees, Bombus terrestris, for floral colour stimuli were studied using artificial flowers. The artificial flowers provided a colour pattern and consisted of a star-shaped corolla and of central colour patches similar to the nectar guide of natural flowers. The innate choice behaviour was assessed in terms of the number of approach flights from some distance towards the artificial flowers and the percentage of approach flights terminating in antennal contact with the floral guide. The colours of the floral guide, the corolla and the background were varied. It was shown that the innate flower colour preference in bumble bees has two components. 1. The frequency of approaches from a distance is correlated with the colour difference between the corolla and the background against which it is presented. If the corolla colour was constant but its background colour varied, the relative attractiveness of the corolla increased with its colour difference to the background. The colour difference assessment underlying this behaviour on a perceptual basis can be attained by means of colour opponent coding, a system well-established in Hymenoptera. 2. The frequency of antennal contacts with the floral guides relative to that of approach flights cannot be accounted for by colour opponent coding alone. Whether the approach flights are interrupted, or whether they end in an antennal contact with the nectar guide is strongly dependent on the direction (sign) of the colour difference, not only its magnitude. The choice behaviour requires a unique perceptual dimension, possibly that of colour saturation or that of hue perception comparable to components of colour perception in humans.     

Modern-day eunuchs: motivations for and consequences of contemporary castration

This article compares the motivations for, and responses to, castration between two groups of males: prostate cancer patients and voluntary modern-day eunuchs with castration paraphilias or other emasculating obsessions. Prostate cancer patients are distressed by the side effects of androgen deprivation and typically strive to hide or deny the effects of castration. In contrast, most voluntary eunuchs are pleased with the results of their emasculations. Despite a suggested association of androgen deprivation with depression, voluntary eunuchs appear to function well, both psychologically and socially. Motivation, rather than physiology, appears to account for these different responses to androgen deprivation.     

Three basic programs for recording,storing, and handling behavioral data

Behavioral studies using observational methods can be improved by the use of microcomputers. Computers are time-saving tools that enhance quantitative assessment of behavior. This is important in primate behavior studies, which typically are long-term and involve large repertoires of behaviors. The present study describes three BASIC programs developed to record, store, and handle behavioral data. This software was created to allow the collection of a library of unabridged sampling sessions. The data-handling programs were designed so that users can effortlessly extract specific information without disturbing the original recordings. Moreover, the programs can be easily translated to any BASIC dialect, so their use is not limited to a particular machine.     

ParStream-seq: An improved method of handling next generation sequence data

The exponential growth of next generation sequencing (NGS) data has put forward the challenge for its storage as well as its efficient and faster analysis. Storing the entire amount of data for a particular experiment and its alignment to the reference genome is an essential step for any quantitative analysis of NGS data. Here, we introduce streaming access technique ‘ParStream-seq’ that splits the bulk sequence data, accessed from a remote repository into short manageable packets followed by executing their alignment process in parallel in each of the compute core. The optimal packet size with fixed number of reads is determined in the stream that maximizes system utilization. Result shows a reduction in the execution time and improvement in the memory footprint. Overall, this streaming access technique provides means to overcome the hurdle of storing the entire volume of sequence data corresponding to a particular experiment, prior to its analysis.     

Prosocial primates: selfish and unselfish motivations

Non-human primates are marked by well-developed prosocial and cooperative tendencies as reflected in the way they support each other in fights, hunt together, share food and console victims of aggression. The proximate motivation behind such behaviour is not to be confused with the ultimate reasons for its evolution. Even if a behaviour is ultimately self-serving, the motivation behind it may be genuinely unselfish. A sharp distinction needs to be drawn, therefore, between (i) altruistic and cooperative behaviour with knowable benefits to the actor, which may lead actors aware of these benefits to seek them by acting cooperatively or altruistically and (ii) altruistic behaviour that offers the actor no knowable rewards. The latter is the case if return benefits occur too unpredictably, too distantly in time or are of an indirect nature, such as increased inclusive fitness. The second category of behaviour can be explained only by assuming an altruistic impulse, which—as in humans—may be born from empathy with the recipient''s need, pain or distress. Empathy, a proximate mechanism for prosocial behaviour that makes one individual share another''s emotional state, is biased the way one would predict from evolutionary theories of cooperation (i.e. by kinship, social closeness and reciprocation). There is increasing evidence in non-human primates (and other mammals) for this proximate mechanism as well as for the unselfish, spontaneous nature of the resulting prosocial tendencies. This paper further reviews observational and experimental evidence for the reciprocity mechanisms that underlie cooperation among non-relatives, for inequity aversion as a constraint on cooperation and on the way defection is dealt with.     

How-possibly explanations as genuine explanations and helpful heuristics: A comment on Forber

Recently, Forber introduced a distinction between two kinds of how-possibly explanation, global and local how-possibly explanation, and argued that both play genuinely explanatory roles in evolutionary biology. In this paper I examine the nature of these two kinds of how-possibly explanations, focusing on the question whether they indeed constitute genuine explanations. I will conclude that one of Forber's kinds of how-possibly explanation may be thought of as a kind of genuine explanation but not as a kind of how-possibly explanation, while the other kind plays a heuristic role and should not be conceived of as a kind of explanation at all.     

Selective feeding by protozoa: model and experimental behaviors and their consequences for population stability

Selective feeding by zooplankton can have profound consequencesfor the stability of grazer and prey populations, as demonstratedby the behavior of plankton dynamics models. We present an analyticalapproach—calculation of prey ratio trajectories—thatreveals unambiguously whether selective feeding behavior isstabilizing (i.e. provides a refuge for preferred prey speciesat low prey concentrations) or destabilizing (i.e. results inelimination of prey populations). Prey ratio trajectories werecalculated for three modeled selective feeding behaviors. Constantselection was consistently destabilizing, while selection behaviorsthat changed inresponse to either prey ratio or prey abundancecould be stabilizing. Batch culture experiments with four protozoangrazer species (three ciliates, one heterotrophic dinoftagellate)demonstrated that protozoa fed selectively in every case, weaklypreferring the larger of the two algal species offered. Stabilizingselection was observed only in the experiment with Favella sp.,however, meaning that only this species altered its selectionbehavior in response to changing experimental conditions. Becauseprotozoa are the major grazers of phytoplankton in many planktonicsystems, our findings indicate that the use of selective feedingbehaviors to stabilize plankton dynamics models needs carefulevaluation. The modeling and graphical techniques presentedhereare a tool for linking further exploration of selective feedingbehaviors with the development of planktondynamics models.     

A computer system for handling data from bacterial sensitivity testing.

A computer system for handling data collected from antibiotic sensitivity testing of clinical bacterial isolates is described. The system allows a rapid handling of the information collected, supplying the ward and laboratory with cummulative data on each patient. The bacteriologist and the clinician are thus suitably armed when creating a rational antibiotic therapy.     

A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.