Using Microbial Microcosms to Study Host–parasite Coevolution

Microbial microcosm experiments with bacteria and their viral parasites allow us to observe host–parasite coevolution in action. Laboratory populations of microbes evolve rapidly, thanks to their short generation times and huge population sizes. By taking advantage of a “living fossil record” stored in the laboratory freezer, we can directly compare the fitness of hosts and parasites with their actual evolutionary ancestors. Such experiments demonstrate that host–parasite coevolution is an important evolutionary force and a cause of strong and divergent natural selection.     

On the Number of Binary Characters Needed to Recover a Phylogeny Using Maximum Parsimony

We give an explicit construction to solve a conjecture of Mike Steel and David Penny that any phylogeny involving N taxa can be recovered unambiguously using on the order of log N binary characters and the method of maximum parsimony. Biologically, this means that homoplasy need not be a deterrent to parsimony methods. Some patterns of homoplasy are phylogenetically informative and can exponentially reduce the amount of data needed to resolve a phylogeny.     

A Molecular Phylogeny of Plesiorycteropus Reassigns the Extinct Mammalian Order ‘Bibymalagasia’

Madagascar is well known for its diverse fauna and flora, being home to many species not found anywhere else in the world. However, its biodiversity in the recent past included a range of extinct enigmatic fauna, such as elephant birds, giant lemurs and dwarfed hippopotami. The ‘Malagasy aardvark’ (Plesiorycteropus) has remained one of Madagascar’s least well-understood extinct species since its discovery in the 19^th century. Initially considered a close relative of the aardvark (Orycteropus) within the order Tubulidentata, more recent morphological analyses challenged this placement on the grounds that the identifiably derived traits supporting this allocation were adaptations to digging rather than shared ancestry. Because the skeletal evidence showed many morphological traits diagnostic of different eutherian mammal orders, they could not be used to resolve its closest relatives. As a result, the genus was tentatively assigned its own taxonomic order ‘Bibymalagasia’, yet how this order relates to other eutherian mammal orders remains unclear despite numerous morphological investigations. This research presents the first known molecular sequence data for Plesiorycteropus, obtained from the bone protein collagen (I), which places the ‘Malagasy aardvark’ as more closely related to tenrecs than aardvarks. More specifically, Plesiorycteropus was recovered within the order Tenrecoidea (golden moles and tenrecs) within Afrotheria, suggesting that the taxonomic order ‘Bibymalagasia’ is obsolete. This research highlights the potential for collagen sequencing in investigating the phylogeny of extinct species as a viable alternative to ancient DNA (aDNA) sequencing, particularly in cases where aDNA cannot be recovered.     

Study on Physiological Mechanism of Using Cottonseed Meal to Improve Salt–Alkali Tolerance of Cotton

Journal of Plant Growth Regulation - Saline–alkali stress is the main environmental factor restricting the growth and production of cotton, one of the most important cash crops in the world....     

Using model systems to unravel host–Pseudomonas aeruginosa interactions

Using model systems in infection biology has led to the discoveries of many pathogen-encoded virulence factors and critical host immune factors to fight pathogenic infections. Studies of the remarkable Pseudomonas aeruginosa bacterium that infects and causes disease in hosts as divergent as humans and plants afford unique opportunities to shed new light on virulence strategies and host defence mechanisms. One of the rationales for using model systems as a discovery tool to characterise bacterial factors driving human infection outcomes is that many P. aeruginosa virulence factors are required for pathogenesis in diverse different hosts. On the other side, many host signalling components, such as the evolutionarily conserved mitogen-activated protein kinases, are involved in immune signalling in a diverse range of hosts. Some model organisms that have less complex immune systems also allow dissection of the direct impacts of innate immunity on host defence without the interference of adaptive immunity. In this review, we start with discussing the occurrence of P. aeruginosa in the environment and the ability of this bacterium to cause disease in various hosts as a natural opportunistic pathogen. We then summarise the use of some model systems to study host defence and P. aeruginosa virulence.     

A Functional Study of Single Mammalian CNS “Synaptic Bouton”

Single CNS neurons could be dissociated with adherent functional synaptic boutons without using any enzyme, namely when preparing a “synaptic bouton.” This allows experimenters to investigate the effects of presynaptic modulators of synaptic transmission with unprecedented case and accuracy. Moreover, a single bouton can be visualized using fluorescent markers and can also be focally stimulated with electrical pulses. In this communication, high voltage-dependent Ca²⁺ channels of nerve endings, as one of experimental examples using the “synaptic bouton” preparation, are described. Ca²⁺ channels belonging to different subtypes, which trigger GABA release from nerve terminals (boutons) projecting to rat hippocampal CA1 pyramidal neurons, were studied. GABA-ergic evoked inhibitory postsynaptic currents (eIPSCs) were recorded; these currents were evoked by focal stimulation of single boutons in mechanically dissociated neurons and by stimulation of a nerve bundle in slice preparations. Nilvadipine, an L-type Ca²⁺ channel blocker, completely inhibited eIPSCs evoked by stimulation of single boutons but exerted no effect on eIPSCs evoked by low-frequency stimulation of the nerve bundle. Nilvadipine did, however, prevent potentiation of the eIPSC amplitude following high-frequency stimulation of the nerve bundles in slice preparations. ω-Conotoxin-GVIA, an N-type Ca²⁺ channel blocker, and ω-Agatoxin-IVA, a P/Q-type Ca²⁺ channel blocker, completely inhibited the eIPSCs in 33.3 and 83.3% of the recordings from single boutons, respectively. In response to low-frequency nerve bundle stimulation in the slice preparation, both ω-Conotoxin-GVIA and ω-Agatoxin-IVA partially reduced the amplitude of eIPSC, and the residual component could be abolished by Cd²⁺. From these results, the following hypotheses could be drawn. (i) The distribution of P/Q- and N-type Ca²⁺ channels at a single bouton is nonuniform; (ii) when a focal stimulation is applied to a single bouton, L-type Ca²⁺ channels play a significant role in generation of action potentials, which subsequently activate P/Q- and N-type Ca²⁺ channels at GABA release sites; and (iii) action potentials conducted through axons in the slice preparation are sufficient to depolarize the bouton membrane, even when L-type Ca²⁺ channels are suppressed. Neirofiziologiya/Neurophysiology, Vol. 37, No. 2, pp. 181–183, March–April, 2005.     

Repair of DNA–Protein Cross-links in Mammalian Cells

DNA–protein cross-links are generated by both endogenous and exogenous DNA damaging agents, as intermediates during normal DNA metabolism, and during abortive base excision repair. Cross-links are relatively common lesions that are lethal when they block progression of DNA polymerases. DNA–protein cross-links may be broadly categorized into four groups by the DNA and protein chemistries near the cross-link and by the source of the cross-link: DNA–protein cross-links may be found (1) in nicked DNA at the 3' end of one strand (topo I), (2) in nicked DNA at the 5' end of one strand (pol beta), (3) at the 5' ends of both strands adjacent to nicks in close proximity (topo II; Spo 11), and (4) in one strand of duplex DNA (UV irradiation; bifunctional carcinogens and chemotherapeutic agents). Repair mechanisms are reasonably well-defined for groups 1 and 3, and suggested for groups 2 and 4. Our work is focused on the recognition and removal of DNA–protein cross-links in duplex DNA (group 4).     

Using synthetic peptides and recombinant collagen to understand DDR–collagen interactions

The discoidin domain receptors, DDR1 and DDR2, are a subfamily of receptor tyrosine kinases that are activated upon binding to collagen. DDR–collagen interactions play an important role in cell proliferation and migration. Over the past few decades, synthetic peptides and recombinant collagen have been developed as tools to study the biophysical characteristics of collagen and various protein–collagen interactions. Herein we review how these techniques have been used to understand DDR–collagen interactions. Using synthetic collagen-like peptides, the GVM-GFO motif has been found to be the major binding site on collagens II and III for DDR1 and DDR2. An X-ray co-crystal structure of the DDR2 DS domain bound to a synthetic collagen-like peptide containing the GVM-GFO motif further provides molecular details of the DDR–collagen interactions. Recombinant collagen has also been used to provide further validation of the GVM-GFO binding motif. Although GVM-GFO has been defined as the minimal binding site, in synthetic peptide studies at least two triplets N-terminal to the essential GVM-GFO binding motif in collagen III sequence are needed for DDR2 activation at high peptide concentrations.     

Community Response of Mammalian Predators and Their Prey to Motorways: Implications for Predator–Prey Dynamics

Understanding the interactions between predators and prey is essential for predicting the effects of disturbances to ecosystems. Motorways produce changes in the surrounding biotic and abiotic environment and hence have multiple impacts on wildlife. Some species are known to change their activity patterns in the proximity of motorways but the implications for the structure of food webs are unknown. This study analyzes the activity patterns of both mammalian predators and their prey species near nine motorways in attempt to clarify how motorways affect the mammalian community. Habitat structural variables were also sampled to control the effects of microhabitat on relative prey abundance. Our results revealed different activity patterns of both predators and prey near motorways that are independent of structural differences in microhabitat. Both the red fox and small mammals were found to use the zone close to the motorways more frequently, whereas lagomorphs and mustelids were less active there. These differences suggest that motorways favor the population of the predator that is most tolerant of human activity, the red fox, whose activity could have both direct and indirect effects on that of other members of the predator and prey community. On the one hand, the red fox seems to act as “top predator” and mustelids to follow a “safety match” strategy avoiding the area close to the motorway where fox is more active. On the other hand, abundances of prey species are negatively associated with the activity of their most frequent predators. This study is the first to assess how the proximity to motorways affects the activity of mammals in two levels of the food web and opens the field for research to understand the processes driving the detected patterns. Moreover, such effects at the community scale should be taken into account when evaluating the impacts of motorways on the surrounding ecosystems.     

Using an α-Bungarotoxin Binding Site Tag to Study GABA A Receptor Membrane Localization and Trafficking

It is increasingly evident that neurotransmitter receptors, including ionotropic GABA A receptors (GABAAR), exhibit highly dynamic trafficking and cell surface mobility^1-7. To study receptor cell surface localization and endocytosis, the technique described here combines the use of fluorescent α-bungarotoxin with cells expressing constructs containing an α-bungarotoxin (Bgt) binding site (BBS). The BBS (WRYYESSLEPYPD) is based on the α subunit of the muscle nicotinic acetylcholine receptor, which binds Bgt with high affinity^8,9. Incorporation of the BBS site allows surface localization and measurements of receptor insertion or removal with application of exogenous fluorescent Bgt, as previously described in the tracking of GABAA and metabotropic GABAB receptors^2,10. In addition to the BBS site, we inserted a pH-sensitive GFP (pHGFP¹¹) between amino acids 4 and 5 of the mature GABAAR subunit by standard molecular biology and PCR cloning strategies (see Figure 1)¹². The BBS is 3'' of the pH-sensitive GFP reporter, separated by a 13-amino acid alanine/proline linker. For trafficking studies described in this publication that are based on fixed samples, the pHGFP serves as a reporter of total tagged GABAAR subunit protein levels, allowing normalization of the Bgt labeled receptor population to total receptor population. This minimizes cell to cell Bgt staining signal variability resulting from higher or lower baseline expression of the tagged GABAAR subunits. Furthermore the pHGFP tag enables easy identification of construct expressing cells for live or fixed imaging experiments.     

Primate Tales: Using Literature to Understand Changes in Human–Primate Relations

Primate species, by and large, are culturally significant icons across their habitat. One of the more prominent expressions of this lies in the revered status of macaques and langurs in South and Southeast Asia, largely because of their religious status in Hinduism. People’s belief in these species’ sanctity often serves to protect them from physical harm or retaliation in conflict situations and thus strongly mediates their conservation. The nature of this interface has changed over the years of mutual interactions between the two groups. Trends in literature are useful markers of sociocultural developments in human life and reflect changes in human views with respect to the world around them. I investigated Tamil language poetical works from southern India to analyze people’s attitudes toward primates and changes in their views of primates over time. My findings suggest that sacredness was not a defining characteristic of human–primate relations in ancient times. The deification of monkeys occurred later and was largely driven by the growing popularity of Ramayana, the Hindu epic. The growing importance of religion in the daily lives of people and increasing urbanization subsequently led to the peripheralization of monkeys in people’s lives and narratives. Monkeys, once considered coinhabitants of a shared landscape, slowly began to be seen as animals with some human-like qualities that represent wild nature. The literary lens is thus a useful tool to map and understand changes in human perceptions of primate species over time and can be a powerful method in ethnoprimatology.     

Using Hidden Markov Models to Improve Quantifying Physical Activity in Accelerometer Data – A Simulation Study

Introduction

The use of accelerometers to objectively measure physical activity (PA) has become the most preferred method of choice in recent years. Traditionally, cutpoints are used to assign impulse counts recorded by the devices to sedentary and activity ranges. Here, hidden Markov models (HMM) are used to improve the cutpoint method to achieve a more accurate identification of the sequence of modes of PA.

Methods

1,000 days of labeled accelerometer data have been simulated. For the simulated data the actual sedentary behavior and activity range of each count is known. The cutpoint method is compared with HMMs based on the Poisson distribution (HMM[Pois]), the generalized Poisson distribution (HMM[GenPois]) and the Gaussian distribution (HMM[Gauss]) with regard to misclassification rate (MCR), bout detection, detection of the number of activities performed during the day and runtime.

Results

The cutpoint method had a misclassification rate (MCR) of 11% followed by HMM[Pois] with 8%, HMM[GenPois] with 3% and HMM[Gauss] having the best MCR with less than 2%. HMM[Gauss] detected the correct number of bouts in 12.8% of the days, HMM[GenPois] in 16.1%, HMM[Pois] and the cutpoint method in none. HMM[GenPois] identified the correct number of activities in 61.3% of the days, whereas HMM[Gauss] only in 26.8%. HMM[Pois] did not identify the correct number at all and seemed to overestimate the number of activities. Runtime varied between 0.01 seconds (cutpoint), 2.0 minutes (HMM[Gauss]) and 14.2 minutes (HMM[GenPois]).

Conclusions

Using simulated data, HMM-based methods were superior in activity classification when compared to the traditional cutpoint method and seem to be appropriate to model accelerometer data. Of the HMM-based methods, HMM[Gauss] seemed to be the most appropriate choice to assess real-life accelerometer data.     

Using short columns to speed up LC–MS quantification in MS binding assays

The present study describes the use of short columns to speed up LC–MS quantification in MS binding assays. The concept of MS binding assays follows closely the principle of traditional radioligand binding but uses MS for the quantification of bound marker thus eliminating the need for a radiolabelled ligand. The general strategy of increasing the throughput of this type of binding assay by the use of short columns is exemplified for NO 711 binding addressing GAT1, the most prevalent GABA transporter in the CNS. Employing short RP-18 columns with the dimension of 20 mm × 2 mm and 10 mm × 2 mm at flow rates up to 1000 μL/min in an isocratic mode retention times of 8–9 s and chromatographic cycle times of 18 s could be achieved. Based on the internal standard [²H₁₀]NO 711 fast chromatography methods were developed for four different columns that enabled quantification of NO 711 in a range from 50 pM up to 5 nM directly out of reconstituted matrix samples without further sample preparation. A validation of the established methods with respect to linearity, intra- and inter-batch accuracy and precision showed that the requirements according to the FDA guideline for bioanalytical methods are met. Furthermore the established short column methods were applied to the quantification of NO 711 in saturation experiments. The results obtained (i.e., K_d- and B_max-values) were almost identical as compared to those determined employing standard column dimension (55 mm × 2 mm).     

Using contact logging devices to explore animal affiliations: Quantifying cow–calf interactions

Understanding animal affiliations has important implications for determining social interactions; an example is maternal interactions within beef production systems. The objective of this study was to test whether contact loggers could be used to identify cow–calf pairs. Fifty-two pairs of Belmont Red cows with calves that were between 1- and 14-days old, were fitted with contact logging devices for 1 week in groups ranging in size from five to nine pairs of cows and calves. The contact logging devices recorded the duration of contacts that were less than 7 m distance between individual animals in the group. There was a highly significant difference in both contact duration and contact frequency between cows and their own calves and cows and all other calves. It is concluded that contact logging devices have the potential to provide useful data on animal affiliations.     

Using yeast to model calcium-related diseases: Example of the Hailey–Hailey disease

Cross-complementation studies offer the possibility to overcome limitations imposed by the inherent complexity of multicellular organisms in the study of human diseases, by taking advantage of simpler model organisms like the budding yeast Saccharomyces cerevisiae. This review deals with, (1) the use of S. cerevisiae as a model organism to study human diseases, (2) yeast-based screening systems for the detection of disease modifiers, (3) Hailey–Hailey as an example of a calcium-related disease, and (4) the presentation of a yeast-based model to search for chemical modifiers of Hailey–Hailey disease. The preliminary experimental data presented and discussed here show that it is possible to use yeast as a model system for Hailey–Hailey disease and suggest that in all likelihood, yeast has the potential to reveal candidate drugs for the treatment of this disorder. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.     

Chronobiological Study of the Pharmacological Response of Rats to Combination Ketamine–Midazolam

Ketamine is commonly administered in combination with benzodiazepines to achieve surgical anaesthesia in rats. The aim of the present study was to analyze the pharmacological response of the combination ketamine–midazolam injected intraperitoneally at different times of day to rats. The study was conducted in July 2003, during the winter in the Southern hemisphere. Female prepuberal Sprague-Dawley rats synchronized to a 12 h light:12 h dark cycle (light, 07:00–19:00 h) were used as experimental animals. A combination treatment of ketamine (40 mg/kg) and midazolam (2 mg/kg) was administered to five different clock-time groups of rats (n = 7/group). Duration of the latency period, ataxia, loss-of-righting reflex (LRR), post-LRR ataxia, and total pharmacological response were assessed by visual assessment. Significant treatment-time differences were detected in the duration of LRR, post-LRR ataxia, and total pharmacological response duration. The longest pharmacological response occurred in rats injected during the light (rest) phase, and the shortest pharmacological response occurred in rats injected during the dark (activity) phase. Cosinor analysis documented circadian rhythmicity in the duration of post-LRR ataxia. The findings of the study indicate the duration of CNS-depression of the ketamine–midazolam combination exhibits treatment-time-dependent variation in the rat.