How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?

Gene regulatory networks (GRNs) play a central role in systems biology, especially in the study of mammalian organ development. One key question remains largely unanswered: Is it possible to infer mammalian causal GRNs using observable gene co-expression patterns alone? We assembled two mouse GRN datasets (embryonic tooth and heart) and matching microarray gene expression profiles to systematically investigate the difficulties of mammalian causal GRN inference. The GRNs were assembled based on pieces of experimental genetic perturbation evidence from manually reading primary research articles. Each piece of perturbation evidence records the qualitative change of the expression of one gene following knock-down or over-expression of another gene. Our data have thorough annotation of tissue types and embryonic stages, as well as the type of regulation (activation, inhibition and no effect), which uniquely allows us to estimate both sensitivity and specificity of the inference of tissue specific causal GRN edges. Using these unprecedented datasets, we found that gene co-expression does not reliably distinguish true positive from false positive interactions, making inference of GRN in mammalian development very difficult. Nonetheless, if we have expression profiling data from genetic or molecular perturbation experiments, such as gene knock-out or signalling stimulation, it is possible to use the set of differentially expressed genes to recover causal regulatory relationships with good sensitivity and specificity. Our result supports the importance of using perturbation experimental data in causal network reconstruction. Furthermore, we showed that causal gene regulatory relationship can be highly cell type or developmental stage specific, suggesting the importance of employing expression profiles from homogeneous cell populations. This study provides essential datasets and empirical evidence to guide the development of new GRN inference methods for mammalian organ development.     

How Long Is Too Long in Contemporary Peer Review? Perspectives from Authors Publishing in Conservation Biology Journals

Delays in peer reviewed publication may have consequences for both assessment of scientific prowess in academia as well as communication of important information to the knowledge receptor community. We present an analysis on the perspectives of authors publishing in conservation biology journals regarding their opinions on the importance of speed in peer-review as well as how to improve review times. Authors were invited to take part in an online questionnaire, of which the data was subjected to both qualitative (open coding, categorizing) and quantitative analyses (generalized linear models). We received 637 responses to 6,547 e-mail invitations sent. Peer-review speed was generally perceived as slow, with authors experiencing a typical turnaround time of 14 weeks while their perceived optimal review time was six weeks. Male and younger respondents seem to have higher expectations of review speed than females and older respondents. The majority of participants attributed lengthy review times to reviewer and editor fatigue, while editor persistence and journal prestige were believed to speed up the review process. Negative consequences of lengthy review times were perceived to be greater for early career researchers and to have impact on author morale (e.g. motivation or frustration). Competition among colleagues was also of concern to respondents. Incentivizing peer-review was among the top suggested alterations to the system along with training graduate students in peer-review, increased editorial persistence, and changes to the norms of peer-review such as opening the peer-review process to the public. It is clear that authors surveyed in this study viewed the peer-review system as under stress and we encourage scientists and publishers to push the envelope for new peer-review models.     

Mass Drug Administration for Trachoma: How Long Is Not Long Enough?

BackgroundBlinding trachoma is targeted for elimination by 2020 using the SAFE strategy (Surgery, Antibiotics, Facial cleanliness, and Environmental improvements). Annual mass drug administration (MDA) with azithromycin is a cornerstone of this strategy. If baseline prevalence of clinical signs of trachomatous inflammation – follicular among 1-9 year-olds (TF1-9) is ≥10% but <30%, the World Health Organization guidelines are for at least 3 annual MDAs; if ≥30%, 5. We assessed the likelihood of achieving the global elimination target of TF1-9 <5% at 3 and 5 year evaluations using program reports.ConclusionsNumber of annual MDAs alone appears insufficient to predict program progress; more information on the effects of baseline prevalence, coverage, and underlying environmental and hygienic conditions is needed. Programs should not skip MDAs, and at prevalences >30%, 7 or more annual MDAs may be required to achieve the target. There are five years left before the 2020 deadline to eliminate blinding trachoma. Low endemic settings are poised to succeed in their elimination goals. However, newly-identified high prevalence districts warrant immediate inclusion in the global program. Intensified application of the SAFE strategy is needed in order to guarantee blinding trachoma elimination by 2020.     

Editorial: Is the dollar ‘Too Big to Fail’?

Dialectical Anthropology -     

Why Is the Substomatal Chamber as Large as It Is?

The rate of CO(2) uptake by the mesophyll is examined as a function of the size of the substomatal chamber. Using the techniques of classical electric circuit analysis and a model in which the uptake is linear in the ambient CO(2) concentration, it is shown that the optimal chamber radius is several times larger than is the pore radius. This is somewhat larger than necessary for the reduction of transpirational water loss, and it offers an explanation for the otherwise inexplicably large size of the chamber.     

On the controversial questions of the taxonomy of Bivalvia (Mollusca): Too many species or too few characters?

Problems emerging in the course of taxonomic studies and species diagnostics of freshwater bivalves are discussed by the example of one of the bivalve groups (the family Unionidae). It is shown that one of the causes of the current, diametrically opposing views on specific and generic systematics of Bivalvia is the fact that researchers revising taxonomic groups ignore complex analysis of several independent characters (conchological, anatomical, biochemical, genetic, etc.).     

Molecular Probes: What Is the Range of Their Interaction with the Environment?

We performed pressure-tuning hole-burning experiments on a modified cytochrome c protein in a glycerol/buffer glass. The shift and the broadening of the holes were investigated for various frequencies within the inhomogeneous band. On the basis of a simple model, we were able to estimate the interaction range between chromophore and protein. It is ~4.5 Å. The parameters that enter the model are the compressibility, the static mean-square displacement, the inhomogeneous width, and the average spectral shift per pressure. From this result and from our experiments on pressure-induced denaturing, we conclude that water molecules have to be brought very close to the chromophore during the denaturation process.     

On the aggregation properties of FMRP--a link with the FXTAS syndrome?

Fragile X mental retardation protein (FMRP) is an RNA binding protein necessary for correct spatiotemporal control of neuronal gene expression in humans. Lack of functional FMRP causes fragile X mental retardation, which is the most common inherited neurodevelopmental disorder in humans. In a previous study, we described the biochemical and biophysical aggregation properties of constructs spanning the conserved region of FMRP and of two other human fragile X related (FXR) proteins, FXR1P and FXR2P. Here, we show that the same regions have an intrinsic tendency to aggregate and spontaneously misfold towards β-rich structures, also under non-destabilizing conditions. These findings pave the way to future studies of the mechanism of formation of FXR-containing ribonucleoprotein granules and suggest a possible link with the as yet poorly understood FXR proteins' associated pathologies.     

How Much Is Too Much? Assessment of Prey Consumption by Magellanic Penguins in Patagonian Colonies

Penguins are major consumers in the southern oceans although quantification of this has been problematic. One suggestion proposes the use of points of inflection in diving profiles (‘wiggles’) for this, a method that has been validated for the estimation of prey consumption by Magellanic penguins (Spheniscus magellanicus) by Simeone and Wilson (2003). Following them, we used wiggles from 31 depth logger-equipped Magellanic penguins foraging from four Patagonian colonies; Punta Norte (PN), Bahía Bustamente (BB), Puerto Deseado (PD) and Puerto San Julián (PSJ), all located in Argentina between 42–49° S, to estimate the prey captured and calculate the catch per unit time (CPUT) for birds foraging during the early chick-rearing period. Numbers of prey caught and CPUT were significantly different between colonies. Birds from PD caught the highest number of prey per foraging trip, with CPUT values of 68±19 prey per hour underwater (almost two times greater than for the three remaining colonies). We modeled consumption from these data and calculate that the world Magellanic penguin population consumes about 2 million tons of prey per year. Possible errors in this calculation are discussed. Despite this, the analysis of wiggles seems a powerful and simple tool to begin to quantify prey consumption by Magellanic penguins, allowing comparison between different breeding sites. The total number of wiggles and/or CPUT do not reflect, by themselves, the availability of food for each colony, as the number of prey consumed by foraging trip is strongly associated with the energy content and wet mass of each colony-specific ‘prey type’. Individuals consuming more profitable prey could be optimizing the time spent underwater, thereby optimizing the energy expenditure associated with the dives.     

How Abnormal Is the Behaviour of Captive,Zoo-Living Chimpanzees?

BACKGROUND: Many captive chimpanzees (Pan troglodytes) show a variety of serious behavioural abnormalities, some of which have been considered as possible signs of compromised mental health. The provision of environmental enrichments aimed at reducing the performance of abnormal behaviours is increasing the norm, with the housing of individuals in (semi-)natural social groups thought to be the most successful of these. Only a few quantitative studies of abnormal behaviour have been conducted, however, particularly for the captive population held in zoological collections. Consequently, a clear picture of the level of abnormal behaviour in zoo-living chimpanzees is lacking. METHODS: We present preliminary findings from a detailed observational study of the behaviour of 40 socially-housed zoo-living chimpanzees from six collections in the United States of America and the United Kingdom. We determined the prevalence, diversity, frequency, and duration of abnormal behaviour from 1200 hours of continuous behavioural data collected by focal animal sampling. RESULTS, CONCLUSION AND SIGNIFICANCE: Our overall finding was that abnormal behaviour was present in all sampled individuals across six independent groups of zoo-living chimpanzees, despite the differences between these groups in size, composition, housing, etc. We found substantial variation between individuals in the frequency and duration of abnormal behaviour, but all individuals engaged in at least some abnormal behaviour and variation across individuals could not be explained by sex, age, rearing history or background (defined as prior housing conditions). Our data support a conclusion that, while most behaviour of zoo-living chimpanzees is 'normal' in that it is typical of their wild counterparts, abnormal behaviour is endemic in this population despite enrichment efforts. We suggest there is an urgent need to understand how the chimpanzee mind copes with captivity, an issue with both scientific and welfare implications.     

How Large is the Probability for the Estimate of a Variance Component to be Negative?

For a balanced one-way classification, where the normally distributed observations obey a random model y_ij=μ+b_i+c_ij with two variance components var (b_i) = δ and var (c_ij) = δ, the probability is given that the analysis of variance estimate of δ will be negative. This probability depends on δ/δ and the degrees of freedom in the ANOVA table. Tables for this probability are given. If the normally distributed observations obey an intra-class correlation model, the probability that the Mean Square between groups is smaller than the Mean Square within groups can also be evaluated from the given tables.     

Supramolecular architecture of cyanobacterial thylakoid membranes: How is the phycobilisome connected with the photosystems?

Cyanobacteria, as the most simple organisms to perform oxygenic photosynthesis differ from higher plants especially with respect to the thylakoid membrane structure and the antenna system used to capture light energy. Cyanobacterial antenna systems, the phycobilisomes (PBS), have been shown to be associated with Photosystem 2 (PS 2) at the cytoplasmic side, forming a PS 2-PBS-supercomplex, the structure of which is not well understood. Based on structural data of PBS and PS 2, a model for such a supercomplex is presented. Its key features are the PS 2 dimer as prerequisite for formation of the supercomplex and the antiparallel orientation of PBS-cores and the two PS 2 monomers which form the contact area within the supercomplex. Possible consequences for the formation of superstructures (PS 2-PBS rows) within the thylakoid membrane under so-called state 1 conditions are discussed. As there are also indications for specific functional connections of PBS with Photosystem 1 (PS 1) under so-called state 2 conditions, we show a model which reconciles the need for a structural interaction between PBS and PS 1 with the difference in structural symmetry (2-fold rotational symmetry of PBS-cores, 3-fold rotational symmetry of trimeric PS 1). Finally, the process of dynamic coupling and uncoupling of PBS to PS 1 and PS 2, based on the presented models, shows analogies to mechanisms for the regulation of photosynthetic electron flow in higher plants-despite the very different organization of their thylakoid membranes in comparison to cyanobacteria.Abbreviations APC allophycocyanin - b ₆ f cytochrome b ₆ f complex - CP chlorophyll protein - FNR ferredoxin-NADP⁺-oxidoreductase - LD linkerprotein-domain - LHC light-harvesting complex - Pc plastocyanin - PC phycocyanin - PD phycobiliprotein-domain - PS 1 Photosystem 1 - PS 2 Photosystem 2 - PBS phycobilisome Dedicated to Prof. Dr. Horst Senger on the occasion of his 65th birthday.     

Low Fasting Triglycerides: Hallmark of the Healthy Large Hip?

Body fat distribution modulates risk for type 2 diabetes mellitus. We evaluated potentially involved metabolic risk factors. In a population of 282 male and 157 female healthy subjects (data from the San Antonio and the European Group of Insulin Resistance (EGIR) study cohorts), we evaluated associations between body fat distribution (assessed by waist and hip circumference) and parameters of lipid‐ and glucose metabolism, including clamp measurements of insulin sensitivity. After stratification for BMI, fasting triglycerides were lower in the presence of a large hip, and higher in a large waist. Persons with the largest BMI (3rd tertile) showed a difference in triglyceride levels of 1.5 vs. 2.4 mmol/l in large vs. small hip circumference groups (P < 0.038), and a difference of 1.5 vs. 1.2 mmol/l in large vs. small waist circumference groups (P < 0.025). A similar analysis did not reveal a difference in insulin sensitivity. Linear regression analyses confirmed the findings; they revealed negative associations between triglycerides and hip, and (for women borderline statistically significant) positive associations between triglycerides and waist, after adjustment for BMI, mutual confounding, and age (β ± s.e.; men: ?0.48 ± 0.005, P < 0.001, and 0.21 ± 0.005, P < 0.05; women: ?0.78 ± 0.007, P < 0.001, and 0.24 ± 0.005, P < 0.065), respectively. Linear regression analyses revealed similar opposite associations with high‐density lipoprotein (HDL)‐cholesterol, though not with glucose, insulin, or insulin sensitivity as measured with the clamp method. In our study population of healthy persons, body fat distribution is associated with fasting triglycerides and HDL‐cholesterol, and not with insulin sensitivity. Metabolic risk of unfavorable body fat distribution may be modulated by lower triglyceride storage capacity.     

On governance in the long-term vegetation process: How to discover the rules?

Ecological practice is telling us that to identify Nature’s rules, we should look for regularities in the resulting effects. Hidden rules are involved and the effects are manifested by compositional, functional, and structural transitions. This paper’s focus is on two conjectures regarding the governance of specific transition components, the first supposedly under global co-ordination, and the second under superimposed site specific instability oscillations. The reality of any apparent regularity in these is the sole condition for the regularity’s acceptance as a rule. Reality is testable but in retrospect only, based on time series analyses. Since long pollen spectra supply the evidence, the time period involved is measured in thousands of years. For maximal usefulness, a spectrum should have a long period length, dated horizons intensely sampled at short time steps, and precisely identified taxa. Period length and time step width matter because both may have a masking effect on the regularities. There is, of course, a natural limit for period length, which is set by the age of the pollen bearing sediments. We completed the analysis of 23 spectra using techniques deemed suitable for testing the conjectures. The spectra originated from sites in the Americas where we found suitable spectra in sufficient numbers and in geographic contiguity from the Arctic region to the Antarctic. The presented results have clear indications that the two conjectures identify real rules. The main body of the paper narrates the analyses and provides explanations. Informative materials, too voluminous for inclusion in the paper, are made available on the Internet at URL: www.vegetationdynamics.com linking to “Appendices Ta”.     

How Much Is Too Little to Detect Impacts? A Case Study of a Nuclear Power Plant

Several approaches have been proposed to assess impacts on natural assemblages. Ideally, the potentially impacted site and multiple reference sites are sampled through time, before and after the impact. Often, however, the lack of information regarding the potential overall impact, the lack of knowledge about the environment in many regions worldwide, budgets constraints and the increasing dimensions of human activities compromise the reliability of the impact assessment. We evaluated the impact, if any, and its extent of a nuclear power plant effluent on sessile epibiota assemblages using a suitable and feasible sampling design with no ‘before’ data and budget and logistic constraints. Assemblages were sampled at multiple times and at increasing distances from the point of the discharge of the effluent. There was a clear and localized effect of the power plant effluent (up to 100 m from the point of the discharge). However, depending on the time of the year, the impact reaches up to 600 m. We found a significantly lower richness of taxa in the Effluent site when compared to other sites. Furthermore, at all times, the variability of assemblages near the discharge was also smaller than in other sites. Although the sampling design used here (in particular the number of replicates) did not allow an unambiguously evaluation of the full extent of the impact in relation to its intensity and temporal variability, the multiple temporal and spatial scales used allowed the detection of some differences in the intensity of the impact, depending on the time of sampling. Our findings greatly contribute to increase the knowledge on the effects of multiple stressors caused by the effluent of a power plant and also have important implications for management strategies and conservation ecology, in general.     

How Is Vaccine Effectiveness Scaled by the Transmission Dynamics of Interacting Pathogen Strains with Cross-Protective Immunity?

Background

Many novel vaccines can cover only a fraction of all antigenic types of a pathogen. Vaccine effectiveness (VE) in the presence of interactions between vaccine strains and others is complicated by the interacting transmission dynamics among all strains. The present study investigated how the VE estimates measured in the field, based on estimated odds ratio or relative risks, are scaled by vaccination coverage and the transmission dynamics in the presence of cross-protective immunity between two strains, i.e. vaccine and non-vaccine strains.

Methodology/Principal Findings

Two different types of epidemiological models, i.e. with and without re-infection by the same antigenic type, were investigated. We computed the relative risk of infection and the odds ratio of vaccination, the latter of which has been measured by indirect cohort method as applied to vaccine effectiveness study of Streptococcus pneumoniae. The VE based on the relative risk was less sensitive to epidemiological dynamics such as cross-protective immunity and vaccination coverage than the VE calculated from the odds ratio, and this was especially the case for the model without re-infection. Vaccine-induced (cross-protective) immunity against a non-vaccine strain appeared to yield the highest impact on the VE estimate calculated from the odds ratio of vaccination.

Conclusion

It is essential to understand the transmission dynamics of non-vaccine strains so that epidemiological methods can appropriately measure both the direct and indirect population impact of vaccination. For pathogens with interacting antigenic types, the most valid estimates of VE, that are unlikely to be biased by the transmission dynamics, may be obtained from longitudinal prospective studies that permit estimation of the VE based on the relative risk of infection among vaccinated compared to unvaccinated individuals.     

How Is Meaning Grounded in the Organism?

In this paper we address the interrelated questions of why and how certain features of an organism’s environment become meaningful to it. We make the case that knowing the biology is essential to understanding the foundation of meaning-making in organisms. We employ Miguel Nicolelis et al’s seminal research on the mammalian somatosensory system to enrich our own concept of brain-objects as the neurobiological intermediary between the environment and the consequent organismic behavior. In the final section, we explain how brain-objects advance the ongoing discussion of what constitutes a biosemiotic system. In general, this paper acknowledges Marcello Barbieri’s call for biology to make room for meaning, and makes a contribution to that end.