When does reproductive interference occur? Predictions and data

Reproductive interference is interspecific sexual interactions that are costly to at least one species involved. Although many studies have reported a substantial fitness cost associated with reproductive interference, suggesting its ecological significance, others have not observed reproductive interference in study species. Reproductive interference that incurs a large fitness cost is more likely to occur during secondary contacts than between long-coexisting species. I first explain the rationale underlying this prediction using existing literature. Next, I present a conceptual framework to classify pairs of interacting species into one of four states, defined by the ecological and evolutionary stabilities of the species pairs. I discuss how the stability states of species pairs are likely to change over time, along with changes in the demographic and evolutionary role of reproductive interference. I then perform literature survey to test the prediction that reproductive interference should be more prevalent in secondary contact. Finally, I discuss the implications of the proposed conceptual framework and literature survey result.     

Campylobacter and fluoroquinolones: a bias data set?

There is no universally accepted standard method for the isolation of Campylobacter spp. and it is considered that currently available isolation media are not yet optimal for the recovery of Campylobacter spp. from a range of sample types. Almost all methods incorporate antibiotics into the isolation media to inhibit growth of other bacteria within the sample. It is established that the incorporation of such antibiotics into isolation media will inhibit the growth of some Campylobacter spp. as well as other bacteria. The results of the use of such suboptimal isolation methods are that the isolates which 'survive' the isolation procedure will be those which: (i) are able to 'out compete' the rest of the bacteria in the sample, i.e. they are able to grow faster; (ii) are resistant to the antibiotics used in the isolation media; and (iii) are randomly selected by the laboratory technician as being a 'typical'Campylobacter spp. It is clear that such a procedure is intrinsically biased and will mean that species resistant to the antibiotics used in the media will be isolated. This introduces real doubt that the bacteria isolated are truly representative of those initially found on the sample. It is also becoming clear that Campylobacter spp. are rather difficult to isolate as pure cultures and many are in fact mixtures of more than one strain. Again this introduces great uncertainty as to the prevalence and distribution of respective species from the different sample types. This is especially true when considering isolation of Campylobacter spp. causing disease in man as there is no certainty that the selected isolate is that which was responsible for disease. The incorporation of antibiotics into the isolation media not only introduces the issue of species bias but perhaps more importantly exposes the Campylobacter spp. to a cocktail of antibiotics thereby providing the potential for them to 'switch on' antibiotic resistance mechanisms. It might be argued that this has always been the case for isolation of Campylobacter spp., however, we know that the antibiotic cocktails used in media over the last 10 years have changed and indeed there was a time when the filtration protocol which didn't use antibiotics was more widely used. As most reports in the literature do not state what methods were used to isolate Campylobacter spp. it is not possible to quantify any relationship between antibiotics used in the isolation media and susceptibility data. An approved method for Campylobacter susceptibility testing was not available until May 2002, all data generated prior to this date will have been generated using non-standard methods. As tremendous variability in the reproducibility data for Campylobacter spp. was observed during the development of the standard agar dilution susceptibility method, data generated with disk diffusion and broth microdilution methods must be considered with caution. It has been shown that, compared with the conventional agar dilution method, the E-test tends to give rise to lower minimal inhibitory concentrations (MICs) for sensitive strains and higher MICs for resistant strains. There are no recommended antibiotic breakpoint concentrations for Campylobacter spp. A breakpoint is used to separate sensitive from resistant strains of bacteria and is thus crucial to any discussion of antibiotic resistance. This discussion is further complicated by introduction of the terms microbiological and clinical breakpoints. While a microbiological breakpoint can be a useful parameter with regard to identifying resistance factors it cannot on its own be used to predict whether that bacteria will respond to treatment from an appropriate antibiotic. Predicting clinical response is a function of the clinical breakpoint which considers the pharmacokinetic profile of the antimicrobial compound, i.e. the concentration of the antimicrobial compound in the body and the MIC. The National Committee for Clinical Laboratory Standards (NCCLS) uses microbiological, pharmacokinetic and clinical data to establish breakpoints, without c and clinical data to establish breakpoints, without such considerations it is not possible to consider what is truly clinically sensitive and resistant. There are no reported studies that have systematically determined appropriate breakpoints for Campylobacter, there are data however, which relate MICs to clinical outcome. It is without dispute that microbiological resistance in Campylobacter spp. occurs as a result of mutation in the gyrA gene with single point mutations most frequently causing a four- to eightfold shift in the MIC. What is also clear is that if a high enough concentration of antimicrobial relative to MIC of the infecting organism can be achieved not only will the parent organism be killed but also the 'resistant' mutant. Considering the above and the concentrations of ciprofloxacin achieved in the gastro-intestinal tract it is not surprising that clinical cure can be demonstrated for organisms with an MIC of 32 microg ml(-1).     

Are all data types and connectivity models created equal? Validating common connectivity approaches with dispersal data

Aim

There is enormous interest in applying connectivity modelling to resistance surfaces for identifying corridors for conservation action. However, the multiple analytical approaches used to estimate resistance surfaces and predict connectivity across resistance surfaces have not been rigorously compared, and it is unclear what methods provide the best inferences about population connectivity. Using a large empirical data set on puma (Puma concolor), we are the first to compare several of the most common approaches for estimating resistance and modelling connectivity and validate them with dispersal data.

Location

Southern California, USA.

Methods

We estimate resistance using presence‐only data, GPS telemetry data from puma home ranges and genetic data using a variety of analytical methods. We model connectivity with cost distance and circuit theory algorithms. We then measure the ability of each data type and connectivity algorithm to capture GPS telemetry points of dispersing pumas.

Results

We found that resource selection functions based on GPS telemetry points and paths outperformed species distribution models when applied using cost distance connectivity algorithms. Point and path selection functions were not statistically different in their performance, but point selection functions were more sensitive to the transformation used to convert relative probability of use to resistance. Point and path selection functions and landscape genetics outperformed other methods when applied with cost distance; no methods outperformed one another with circuit theory.

Main conclusions

We conclude that path or point selection functions, or landscape genetic models, should be used to estimate landscape resistance for wildlife. In cases where resource limitations prohibit the collection of GPS collar or genetic data, our results suggest that species distribution models, while weaker, may still be sufficient for resistance estimation. We recommend the use of cost distance‐based approaches, such as least‐cost corridors and resistant kernels, for estimating connectivity and identifying functional corridors for terrestrial wildlife.

     

α-Thalassaemia in Tunisia: some epidemiological and molecular data

Unlike the other haemoglobinopathies, few researches have been published concerning α-thalassaemia in Tunisia. The aim of the present work is to acquire further data concerning α-thalassaemia prevalence and molecular defects spectrum in Tunisia, by collecting and studying several kinds of samples carrying α-thalassaemia. The first survey conducted on 529 cord blood samples using cellulose acetate electrophoresis, have displayed the prevalence of 7.38% Hb Bart’s carriers at birth. Molecular analyses were conducted by PCR and DNA sequencing on 20 families’ cases from the above survey carrying the Hb Bart’s at birth and on 10 Hb H diseased patients. The results showed six α-globin gene molecular defects and were responsible for α-thalassaemia: -α^3.7, - -^MedI, α^TSaudi, α₂^{cd23GAG→Stop}, Hb Greone Hart: α₁^119CCT→TCT corresponding to 11 genotypes out of which two are responsible for Hb H disease (- -^Med/-α^3.7) and (α^TSaudiα/α^TSaudiα) and a newly described polymorphism: α^+6C→G. The geographical repartition of α-thal carriers showed that the -α^3.7 deletion is distributed all over the country, respectively the α^HphI and α^TSaudi seem to be more frequent in the central region of the northeast region. The haematological and clinical data showed a moderate phenotype with a late age of diagnosis for Hb H disease. This work had permitted, in addition to an overview on α-thalassaemia in the country, the optimization of protocols for α-thalassaemia detection in our lab, allowing further investigations concerning phenotype-genotype correlation in sickle cell disease or β-thalassaemia.     

Is DIA proteomics data FAIR? Current data sharing practices,available bioinformatics infrastructure and recommendations for the future

Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in, for example, instrumentation and data analysis approaches. However, there are many improvements that are still possible for DIA data in the area of the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include more tailored data sharing practices and open data standards since public databases and data standards for proteomics were mostly designed with DDA data in mind. Here we first describe the current state of the art in the context of FAIR data for proteomics in general, and for DIA approaches in particular. For improving the current situation for DIA data, we make the following recommendations for the future: (i) development of an open data standard for spectral libraries; (ii) make mandatory the availability of the spectral libraries used in DIA experiments in ProteomeXchange resources; (iii) improve the support for DIA data in the data standards developed by the Proteomics Standards Initiative; and (iv) improve the support for DIA datasets in ProteomeXchange resources, including more tailored metadata requirements.     

Service-oriented execution model supporting data sharing and adaptive query processing

To deal with the environment’s heterogeneity, information providers usually offer access to their data by publishing Web services in the domain of pervasive computing. Therefore, to support applications that need to combine data from a diverse range of sources, pervasive computing requires a middleware to query multiple Web services. There exist works that have been investigating on generating optimal query plans. We however in this paper propose a query execution model, called PQModel, to optimize the process of query execution over Web Services. In other words, we attempt to improve query efficiency from the aspect of optimizing the execution processing of query plans.     

Sampling of cardiovascular data; how often and how much?

Long-term measurement of cardiovascular variables by telemetry in laboratory animals has become indispensable in recent years. However, limited battery life and management of large volumes of recorded data are major drawbacks. These limitations can often be overcome by intermittent sampling of data. The question is, how much data does one need to collect to accurately reflect the underlying average value? To investigate this, 24-h continuous recordings of rabbit heart rate, arterial pressure, and integrated renal sympathetic nerve activity (RSNA) were resampled using a variety of protocols that differed with respect to the number of individual sampling periods used and the total amount of time that was sampled. The absolute percentage errors of estimates of the daily mean, standard deviation, and interquartile range were calculated for each sampling protocol. A similar analysis was repeated using arterial pressure data from rats. The results show that the number of sampling periods spread throughout the day had more effect than the total amount of data recorded. For example, just 2 h of total sampling time spread over 12 evenly spaced 10-min periods gave estimates of the daily mean of blood pressure and heart rate with <1% error and RSNA with <3% error. We show that accurate estimates of the daily mean of arterial pressure, heart rate, and RSNA can all be made using scheduled recording, and we recommend recording a minimum of 2 h/day spread over a number of periods throughout the day.     

Maternal and environmental effects on offspring phenotypes in an oviparous lizard: do field data corroborate laboratory data?

A vast literature suggests that maternal factors and egg incubation conditions have substantial effects on offspring phenotypes in oviparous species. However, many studies that evaluate these effects have relied on experimental conditions that are rarely, if ever, encountered under natural conditions. To address this issue, we evaluated relationships among maternal factors, natural nest conditions, egg development in the field, and the resultant offspring phenotypes in a lizard with temperature-dependent sex determination, the jacky dragon (Amphibolurus muricatus, Agamidae). Many, but not all, of the relationships shown in our field-based study corroborate results from laboratory-based experiments. Offspring body size was affected primarily by egg size at oviposition, as well as by water uptake by eggs, rather than by environmental variables measured within the nest. Date of oviposition was related to offspring growth rate and body size prior to the onset of winter; this relationship is likely mediated through an influence on the timing of hatching. Nest temperature generated substantial variation in egg survival; nests that experienced higher temperatures and higher thermal fluctuations suffered relatively high egg mortality. Contrary to results from laboratory incubation, however, nest temperature did not predict offspring sex ratios. Hence, although many results from this field study corroborate those from the laboratory, caution is needed when extrapolating laboratory-incubation results to field conditions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

DNA polymerases and SOS mutagenesis: can one reconcile the biochemical and genetic data?

Until recently, it had been concluded from genetic evidence that DNA polymerase III (Pol III, the main replicative polymerase in E. coli) was also responsible for mutagenic translesion synthesis on damaged templates, albeit under the influence of inducible proteins UmuD' and UmuC. Now it appears that these proteins themselves have polymerase activity (and are now known as Pol V) and can carry out translesion synthesis in vitro in the absence of Pol III. Here I discuss the apparent contradictions between genetics and biochemistry with regard to the role of Pol III in translesion synthesis. Does Pol V interact with Pol III and constitute an alternative component of the replication factory (replisome)? Where do the other three known polymerases fit in? What devices does the cell have to ensure that the "right" polymerase is used in a given situation? The debate about the role of Pol III in translesion synthesis reveals a deeper divide between models that interpret everything in terms of mass action effects and those that embrace a replisome held together by protein-protein interactions and located as a structural entity within the cell.     

Analysis of plastid and nuclear DNA data in plant phylogenetics——evaluation and improvement

Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.     

D3: The Dispersal and Diaspore Database – Baseline data and statistics on seed dispersal

Seed dispersal is hard to measure, and there is still a lack of knowledge about dispersal-related traits of plant species. Therefore, we developed D³, the Dispersal and Diaspore Database (available at www.seed-dispersal.info), which aims at simplifying ecological and evolutionary analyses by providing and integrating various items related to seed dispersal: empirical studies, functional traits, image analyses and ranking indices (quantifying the adaptation to dispersal modes).Currently, the database includes data for more than 5000 taxa and 33 items as well as digital images of diaspores (i.e. the dispersal units), seeds, fruits and infructescences. The included items cover common traits like diaspore mass, size, shape, terminal velocity and seed number per diaspore. Furthermore, we present newly or further developed items like ecomorphological categorizations of the diaspore and fruit as well as information from literature on prevailing dispersal modes. Finally, we introduce several items which are not covered in other databases yet: surface structure and form of the diaspore, the exposure of the diaspores in the infructescence and dispersal rankings. Dispersal rankings allow estimations of how well certain species are adapted to a specific dispersal mode in comparison to a larger species set. They are calculated as the percentile rank of an indicator of species’ dispersal potential in relation to a larger species set.Especially for the new and further developed items we outline the basic concepts in detail, describe the measurement and categorization methods and show how to interpret and integrate these data for single species as well as for larger species sets. Thereby, we calculate baseline statistics of seed dispersal of the Central European flora. We found that diaspores of 72% of the taxa show specializations related to long-distance dispersal, i.e. most often elongated appendages or nutrient-rich tissues. Diaspore masses, sizes and terminal velocities vary over several orders of magnitude and can be approximated by lognormal distributions.     

The discharge letter and data collection — A method for avoiding duplication

It frequently happens that following a patient consultation similar data are recorded in a number of ways in a number of places. This paper describes a method which has been used in one busy clinic to capture this data only once, effecting a saving in consultant's time, avoiding delay in data capture and ensuring consistency of databases. The implementation, using a mixture of custom programs and commercial database software, is discussed. Examples of the sort of data input and user interfaces and some future directions for extension are given. Limitations of commercial packages encountered are mentioned.     

Which clinical and experimental data link temporal lobe epilepsy with depression?

The association of temporal lobe epilepsy with depression and other neuropsychiatric disorders has been known since the early beginnings of neurology and psychiatry. However, only recently have in vivo and ex vivo techniques such as Positron Emission Tomography, Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy in combination with refined animal models and behavioral tests made it possible to identify an emerging pattern of common pathophysiological mechanisms. We now have growing evidence that in both disorders altered interaction of serotonergic and noradrenergic neurons with glutamatergic systems is associated with abnormal neuronal circuits and hyperexcitability. Neuronal hyperexcitability can possibly evoke seizure activity as well as disturbed emotions. Moreover, decreased synaptic levels of neurotransmitters and high glucocorticoid levels influence intracellular signaling pathways such as cAMP, causing disturbances of brain-derived and other neurotrophic factors. These may be associated with hippocampal atrophy seen on Magnetic Resonance Imaging and memory impairment as well as altered fear processing and transient hypertrophy of the amygdala. Positron Emission Tomography studies additionally suggest hypometabolism of glucose in temporal and frontal lobes. Last, but not least, in temporal lobe epilepsy and depression astrocytes play a role that reaches far beyond their involvement in hippocampal sclerosis and ultimately, therapeutic regulation of glial-neuronal interactions may be a target for future research. All these mechanisms are strongly intertwined and probably bidirectional such that the structural and functional alterations from one disease increase the risk for developing the other. This review provides an integrative update of the most relevant experimental and clinical data on temporal lobe epilepsy and its association with depression.     

Do cladistic and morphometric data capture common patterns of morphological disparity?

The distinctly non‐random diversity of organismal form manifests itself in discrete clusters of taxa that share a common body plan. As a result, analyses of disparity require a scalable comparative framework. The difficulties of applying geometric morphometrics to disparity analyses of groups with vastly divergent body plans are overcome partly by the use of cladistic characters. Character‐based disparity analyses have become increasingly popular, but it is not clear how they are affected by character coding strategies or revisions of primary homology statements. Indeed, whether cladistic and morphometric data capture similar patterns of morphological variation remains a moot point. To address this issue, we employ both cladistic and geometric morphometric data in an exploratory study of disparity focussing on caecilian amphibians. Our results show no impact on relative intertaxon distances when different coding strategies for cladistic characters were used or when revised concepts of homology were considered. In all instances, we found no statistically significant difference between pairwise Euclidean and Procrustes distances, although the strength of the correlation among distance matrices varied. This suggests that cladistic and geometric morphometric data appear to summarize morphological variation in comparable ways. Our results support the use of cladistic data for characterizing organismal disparity.