When Less is More: Red Algae as Models for Studying Gene Loss and Genome Evolution in Eukaryotes

Genome evolution is usually viewed through the lens of growth in size and complexity over time, exemplified by plants and animals. In contrast, genome reduction is associated with a narrowing of ecological potential, such as in parasites and endosymbionts. But, can nuclear genome reduction also occur in, and potentially underpin a major radiation of free-living eukaryotes? An intriguing example of this phenomenon is provided by the red algae (Rhodophyta) that have lost many conserved pathways such as for flagellar motility, macroautophagy regulation, and phytochrome based light sensing. This anciently diverged, species-rich, and ecologically important algal lineage has undergone at least two rounds of large-scale genome reduction during its >1 billion-year evolutionary history. Here, using recent analyses of genome data, we review knowledge about the evolutionary trajectory of red algal nuclear and organelle gene inventories and plastid encoded autocatalytic introns. We compare and contrast Rhodophyta genome evolution to Viridiplantae (green algae and plants), both of which are members of the Archaeplastida, and highlight their divergent paths. We also discuss evidence for the speculative hypothesis that reduction in red algal plastid genome size through endosymbiotic gene transfer is counteracted by ongoing selection for compact nuclear genomes in red algae. Finally, we describe how the spliceosomal intron splicing apparatus provides an example of “evolution in action” in Rhodophyta and how the overall constraints on genome size in this lineage has left significant imprints on this key step in RNA maturation. Our review reveals the red algae to be an exciting, yet under-studied model that offers numerous novel insights as well as many unanswered questions that remain to be explored using modern genomic, genetic, and biochemical methods. The fact that a speciose lineage of free-living eukaryotes has spread throughout many aquatic habitats after having lost about 25% of its primordial gene inventory challenges us to elucidate the mechanisms underlying this remarkable feat.     

Maximum Temperature Limits for Acidophilic, Mesophilic Bacteria in Biological Leaching Systems

The maximum temperature for growth (T_max) was determined for pure and mixed cultures of acidophilic thiobacilli. The experimental system was based on incubating the cultures in liquid media exposed to a linear temperature gradient. The T_max values varied within the range of 36.1 to 43.6°C.     

Can Willingness and Hands-on Work Together? Teaching Biological Evolution and Dealing with Barriers

This qualitative research aims at first defining how pre-service science teachers think regarding the theory of evolution (TOE) with a particular hands-on and minds-on activity (The article by O’Brien (Am Biol Teach 62(8):578–582, 2000) entitled A toilet paper timeline of evolution: 5 E cycle on the concept of scale is modified and applied in the present research as an intervention process.) Finally, specific suggestions in instructional techniques are offered based on a geological time scale. At the end of intervention, the research follows how participants respond to what they found out or came across. If participants had common misconceptions regarding the TOE, these are revealed. The present research was conducted in two spring semesters of 2009 and 2010 in a geology course. The participant number of the study was 129. The research lasted three weeks. Research results showed that participants were generally misinformed regarding conceptual knowledge of the TOE. Approximately half of the participants did not believe (the term believing in or acceptance of the TOE does not affect research findings) in the TOE. Mostly, they thought that there is no place for human evolution in Islam. Few of them could reconcile scientific information with their own Islamic point of view. Even though they did not believe in the TOE, most of them accepted that they did not have adequate knowledge regarding the TOE. They mostly said they were shocked about the first appearance of human beings in the geological time scale, which is the main issue in the present research. After intervention, conceptual change was considerable, though this is a secondary concern. The results also show that even though students were quite prejudiced regarding the TOE, they were ready to explore it deeply. Such concrete activities might be helpful to push students to think over the TOE. However, there are numerous barriers such as ill-prepared science textbooks and websites, unwillingness of instructors, and official policy of the Ministry of National Education.     

Hypotheses Derived from Morphological Data: When and How They Are Useful

SYNOPSIS. This paper discusses the validity of hypotheses basedon morphological data,and distinguishes between hypotheses,which are testable, and speculation, which is not. Specificexamples from the mammalian auditory system are examined: arecently evolved, highly derived character (enlarged middleears in desert rodents); and an older, more general character(the inner and outer hair cells of the mammalian organ of Corti).It is concluded that morphologically-based hypotheses are powerfuland important when accompanied by experimental data.     

Sparse Sampling and Maximum Likelihood Estimation for Boolean Models

A condition for practical independence of contact distribution functions in Boolean models is obtained. This result allows the authors to use maximum likelihcod methods, via sparse sampling, for estimating unknown parameters of an isotropic Boolean model. The second part of this paper is devoted to a simulation study of the proposed method. AMS classification: 60D05     

Regulatory Influences on Environmental Protection: Why Shipping Companies Comply and When They Don't

This article reports the findings of an empirical study on the regulation of ship-source pollution at one United Kingdom-based global ship management company. In examining the corporate response of the case-study company, particular attention is given to the regulatory influences promoting such compliance as expressed in the views of company executives. The findings show that both legal regulatory pressures and customer demands are important factors in encouraging the company to comply with environmental requirements. However, the study also revealed that compliance with environmental requirements ultimately depends on the way in which individual companies adapt to different national regulatory and enforcement regimes.     

Mouse Models for Studying the Formation and Propagation of Prions

Prions are self-propagating protein conformers that cause a variety of neurodegenerative disorders in humans and animals. Mouse models have played key roles in deciphering the biology of prions and in assessing candidate therapeutics. The development of transgenic mice that form prions spontaneously in the brain has advanced our understanding of sporadic and genetic prion diseases. Furthermore, the realization that many proteins can become prions has necessitated the development of mouse models for assessing the potential transmissibility of common neurodegenerative diseases. As the universe of prion diseases continues to expand, mouse models will remain crucial for interrogating these devastating illnesses.     

Rats Work for Food They then Reject: Support for the Information-primacy Approach to Learned Industriousness

There is good evidence that in many situations, animals prefer to work for food even when identical food is freely available. This phenomenon is called ‘learned industriousness’ or ‘contrafreeloading’ and has been found in several species. This study shows that wild rats will also work hard for contaminated food that they associate with sickness and subsequently reject, even when wholesome food is continuously available at no extra cost. Seven wild rats (Rattus novegicus) lived for 4 wk in cages containing two operant levers and associated pellet dispensers. The rats earned all their food by lever pressing for 45-mg food pellets on a variable-interval 10 s (VI10s) schedule in each dispenser. After 1 wk, pellets containing a sub-lethal dose of an acute rodenticide were available for 12 h (the test period) from the preferred dispenser, before being replaced by normal food pellets. This procedure was repeated 1 wk and 4 wk later. The number of lever presses, pellets delivered, and pellets consumed at each dispenser were recorded for 12 h prior to the test period, during the 12-h test period, and 12 h after the test period. The rats quickly learned to shift their feeding preference during the test period away from the dispenser that provided the rodenticide pellets. However, during the second half of the test period, lever pressing at this dispenser increased, even though the pellets thereby obtained were still rejected. This divergence between the lever pressing rate and the pellet consumption rate increased over the three trials. This ‘learned-industriousness’ behaviour is not easily explained by the self-reinforcing hypothesis, by the obligate species-specific response hypothesis, or as some artefact of the operant situation. It is suggested that the lever pressing towards the end of the trial, for pellets that were rejected, enabled the animals to gather information about a rare, but very important, event, namely, the presence of dangerous food at a previously preferred and normally safe feeding site. The data lend support to the information-primacy theory of learned industriousness.     

The Effect of Biological Age on Professional Work Capacity: Report II. Biological Age and Physical Work Ability

The possibility of a prognostic estimation of the body's functional state based on comparative analysis of biological age measured by physical work ability parameters in truck drivers was considered. The dependence of the time course of work ability of the people examined on the calendar age and duration of their employment as drivers was studied. It was found that the range of adaptive responses of the cardiovascular system (CVS) to submaximal physical load narrowed in professional drivers earlier than in the control group. A risk group exhibiting signs of premature aging was revealed. It consisted of 40- to 49-year-old persons who had worked as drivers for 15–19 years. It was demonstrated that the approaches proposed are promising for estimating individual aging rates based on the parameters of work ability and for development of prophylactic measures aimed at the prevention of premature and/or accelerated aging of workers.     

Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

Motivation

Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins) others generic (e.g., ‘Homo sapiens’). Generic concepts may play important roles in automated information retrieval, extraction, and inference but may also result in concept overload and confound retrieval and reasoning with low-relevance or even spurious links. Here, we attempted to optimize the retrieval performance for protein-protein interactions (PPI) by filtering generic concepts (node filtering) or links to generic concepts (edge filtering) from a weighted semantic network. First, we defined metrics based on network properties that quantify the specificity of concepts. Then using these metrics, we systematically filtered generic information from the network while monitoring retrieval performance of known protein-protein interactions. We also systematically filtered specific information from the network (inverse filtering), and assessed the retrieval performance of networks composed of generic information alone.

Results

Filtering generic or specific information induced a two-phase response in retrieval performance: initially the effects of filtering were minimal but beyond a critical threshold network performance suddenly drops. Contrary to expectations, networks composed exclusively of generic information demonstrated retrieval performance comparable to unfiltered networks that also contain specific concepts. Furthermore, an analysis using individual generic concepts demonstrated that they can effectively support the retrieval of known protein-protein interactions. For instance the concept “binding” is indicative for PPI retrieval and the concept “mutation abnormality” is indicative for gene-disease associations.

Conclusion

Generic concepts are important for information retrieval and cannot be removed from semantic networks without negative impact on retrieval performance.     

The Large, Free-living Amoebae: Wonderful Cells for Biological Studies

The large, free-living amoebae have been widely used as model cells for studying a variety of biological phenomena, including cell motility, nucleocytoplasmic interactions, membrane function, and symbiosis. Results of studies by our group on amoebae as moving cells, as material for micrurgical manipulations, and as hosts for intracellular symbionts are summarized here. In particular, our recent studies of the amoeba as a microcosm, in which spontaneously infecting foreign microbes have become integrated as necessary cell components, are described in some detail. These processes have involved an initial microbial infection, mutual adaptation by the host and symbionts, and development of obligatory symbiosis. Evidence is presented to show that symbiont-derived macromolecules are involved in the protection of symbionts from digestion, the symbionts have acquired regulatory elements on their chromosomal genes to enhance production of beneficial gene products, and symbionts apparently utilize host-derived macromolecules to their benefit. These studies involved morphological observations both at light and electron microscopic levels, physiological and genetic studies, production and use of poly- and monoclonal antibodies, and molecular-biological approaches including gene cloning and sequencing. It is shown that amoebae are uniquely suited as model cells with which to study these phenomena.     

Predictive Models for Freshwater Biological Assessment: Statistical Approaches,Biological Elements and the Iberian Peninsula Experience: A Review

In the last three decades, predictive models have been developed and applied worldwide for freshwater bioassessment. They consist of statistical tools that follow the concept of the Reference Condition Approach. Composed of several sequential steps, these assessment tools assess the deviation of given site assemblages from the expected biological condition in the absence of human disturbance. The most common approaches (RIVPACS/AUSRIVAS and BEAST) are based on a posteriori classifications that use the biological composition of a community to classify reference sites in groups, and afterwards to establish which environmental features best discriminate the biological groups obtained. Here, we review the predictive modeling procedures used in freshwaters bioassessment (RIVPACS/AUSRIVAS, BEAST, ANNA, Artificial Neural Networks, Bayesian Belief Networks and others) as well as the biological elements to which they have been applied. We also review the Spanish and Portuguese experiences in the development and application of predictive models, with particular attention to regional environmental conditions, the different modeling approaches, and the available implementation tools. Moreover, and considering the natural continuity within the Iberian Peninsula (which include several transnational rivers), we discuss the possibilities of the development of common predictive models across the region, considering all factors that may influence their performance, such as the target scale used to develop the models (regional or peninsular); common reference criteria; sampling and sorting procedures; the taxonomic resolution used in the models; the temporal variability (mainly in the Iberian Mediterranean region); and the biological elements to consider. We concluded that there are good technical conditions for the implementations of a common predictive approach throughout the Iberian Peninsula, which should allow a global biological assessment of streams with different biological elements and seasons that could be used by water managers in the context of the Water Framework Directive. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

All Together Now: The Need for a Combined Empirical and Modeling Approach When Studying Primate Group Coordination

Studies of collective decision making attempt to explain the simultaneous behaviors of many individuals and how these contribute to the behavior observed at a collective level. However, this can be problematic to achieve given the general constraints of field or experimental data. This is particularly the case for primates, and results in limited reproducibility of events and it is difficult to separate the effects of different variables. Advocates of theoretical models have proposed that simple rules of interaction successfully reproduce different phases of group movement and the transitions between them, and greatly contribute to our knowledge of complex phenomena. Models can simulate practically any situation and tell us what response would emerge from it, including complex situations such as group decision making. The general heuristic value of these models has been universally recognized. However, the modeling approach tends to oversimplify real situations, and very few biological validations yet exist. I here suggest that it is essential to confront theoretical results with real data and that the combination of the 2 approaches will substantially improve our comprehension of collective decision making.     

Unmanned Aircraft Systems for Studying Spatial Abundance of Ungulates: Relevance to Spatial Epidemiology

Complex ecological and epidemiological systems require multidisciplinary and innovative research. Low cost unmanned aircraft systems (UAS) can provide information on the spatial pattern of hosts’ distribution and abundance, which is crucial as regards modelling the determinants of disease transmission and persistence on a fine spatial scale. In this context we have studied the spatial epidemiology of tuberculosis (TB) in the ungulate community of Doñana National Park (South-western Spain) by modelling species host (red deer, fallow deer and cattle) abundance at fine spatial scale. The use of UAS high-resolution images has allowed us to collect data to model the environmental determinants of host abundance, and in a further step to evaluate their relationships with the spatial risk of TB throughout the ungulate community. We discuss the ecological, epidemiological and logistic conditions under which UAS may contribute to study the wildlife/livestock sanitary interface, where the spatial aggregation of hosts becomes crucial. These findings are relevant for planning and implementing research, fundamentally when managing disease in multi-host systems, and focusing on risky areas. Therefore, managers should prioritize the implementation of control strategies to reduce disease of conservation, economic and social relevance.