What's on the horizon for macroecology?

Over the last two decades, macroecology – the analysis of large‐scale, multi‐species ecological patterns and processes – has established itself as a major line of biological research. Analyses of statistical links between environmental variables and biotic responses have long and successfully been employed as a main approach, but new developments are due to be utilized. Scanning the horizon of macroecology, we identified four challenges that will probably play a major role in the future. We support our claims by examples and bibliographic analyses. 1) Integrating the past into macroecological analyses, e.g. by using paleontological or phylogenetic information or by applying methods from historical biogeography, will sharpen our understanding of the underlying reasons for contemporary patterns. 2) Explicit consideration of the local processes that lead to the observed larger‐scale patterns is necessary to understand the fine‐grain variability found in nature, and will enable better prediction of future patterns (e.g. under environmental change conditions). 3) Macroecology is dependent on large‐scale, high quality data from a broad spectrum of taxa and regions. More available data sources need to be tapped and new, small‐grain large‐extent data need to be collected. 4) Although macroecology already lead to mainstreaming cutting‐edge statistical analysis techniques, we find that more sophisticated methods are needed to account for the biases inherent to sampling at large scale. Bayesian methods may be particularly suitable to address these challenges. To continue the vigorous development of the macroecological research agenda, it is time to address these challenges and to avoid becoming too complacent with current achievements.     

Does foliage on the same branch compete for the same water? Experiments on Douglas-fir trees

Do branchlets within a branch have autonomous water supplies, or do they share a common water supply system? We hypothesized that if branchlets shared a common water supply, then stomatal conductance (g_s) on sunlit foliage would increase with reduced transpiration of competing foliage on the branch. We reduced transpiration of other foliage on the branch through bagging and shading, and we monitored the gas-exchange responses of the remaining sunlit foliage on the branch relative to control branches for several age classes of Douglas-fir trees (aged ~10 years, 20 years, and 450 years old). Contrary to our hypothesis, we found no increases in g_s in either young or old trees following transient reductions in the amount of transpiring leaf area. The diurnal change in water potential, mid-day stomatal closure and associated photosynthetic decline occurred at the same time and were of the same magnitude on both treated and untreated branches, with the exception of photosynthesis in one 450-year-old tree. Hydraulic conductance measurements of branch junctions indicate that xylem within branches is only partially interconnected which would reduce the effectiveness of shading as a means of increasing water supply to the remaining sunlit foliage. The lack of a response implies that when a branch is in partial shade, the remaining sunlit foliage has no advantage with respect to water status over foliage on a branch completely in the sun.     

Proximate perspectives on the evolution of female aggression: good for the gander,good for the goose?

Female–female aggression often functions in competition over reproductive or social benefits, but the proximate mechanisms of this apparently adaptive behaviour are not well understood. The sex steroid hormone testosterone (T) and its metabolites are well-established mediators of male–male aggression, and several lines of evidence suggest that T-mediated mechanisms may apply to females as well. However, a key question is whether mechanisms of female aggression primarily reflect correlated evolutionary responses to selection acting on males, or whether direct selection acting on females has made modifications to these mechanisms that are adaptive in light of female life history. Here, I examine the degree to which female aggression is mediated at the level of T production, target tissue sensitivity to T, or downstream genomic responses in order to test the hypothesis that selection favours mechanisms that facilitate female aggression while minimizing the costs of systemically elevated T. I draw heavily from avian systems, including the dark-eyed junco (Junco hyemalis), as well as other organisms in which these mechanisms have been well studied from an evolutionary/ecological perspective in both sexes. Findings reveal that the sexes share many behavioural and hormonal mechanisms, though several patterns also suggest sex-specific adaptation. I argue that greater attention to multiple levels of analysis—from hormone to receptor to gene network, including analyses of individual variation that represents the raw material of evolutionary change—will be a fruitful path for understanding mechanisms of behavioural regulation and intersexual coevolution.     

Advancement on techniques for the separation and maintenance of the red imported fire ant colonies

Advancement has recently been made on the techniques for separating and maintaining colonies of red imported fire ants, Solenopsis invicta Buren. A new brood rescue method significantly improved the efficiency in separating colony from mound soil. Furthermore, a new method was developed to separate brood from the colony using fire ant repellants. Finally, a cost-effective method was developed to coat containers with diluted Fluon （AGC Chemicals America, Inc, Moorestown, NJ, USA）, an aqueous polytetrafluoroethylene, to prevent housed ants from escaping a container. Usually the original Fluon solution is directly applied to the wall of the containers. Reduced concentrations of Fhion were found to be equally effective in preventing ant escape. The use of diluted Fluon solutions to coat the containers was recommended because of environmental and cost-saving benefits. Application of these new techniques can significantly reduce labor, cost and environmental contamination. This review paper collates all the new techniques in one reference which readers can use as a manual.     

What constitutes the signal for the initiation of protein synthesis on Escherichia coli mRNAs?

Small DNA fragments (60 to 80 nucleotides), randomly obtained from a collection of 14 catabolic, biosynthetic or regulatory Escherichia coli genes, have been shot-gun cloned in place of the lacZ ribosome binding site. A total of 47 recombinants showing substantial beta-galactosidase synthesis (at least 1/30th of the wild-type) were isolated, and their newly acquired translational starts were characterized. Of these, 46 were found to carry a ribosome binding site from one of the original genes, and only one, a non-natural start. Moreover, 12 out of the 14 natural starts were found. The two that were not found are the only ones lacking a Shine-Dalgarno element. So, real starts are generally active in the lac mRNA, whereas the many sites (approx. 100 in this gene collection) that carry a Shine-Dalgarno element followed by AUG or GUG but are located in intra- or intergenic regions, or on non-transcribed strands, are inactive. I conclude that: (1) these "false" starts, being strongly discriminated against in the lac message, are presumably also inactive in their original mRNAs; (2) the discriminating information, being portable from one mRNA to another, must be contained within a small DNA region surrounding the starts. Indeed, I further show that it generally lies within a sequence of about 35 nucleotides bracketing real starts; and (3) this information must have a larger effect on initiation than the exact structure of the mRNA, because the discrimination persists despite a complete change of this structure. Previous statistical analysis has shown that real starts differ from false starts in having a non-random sequence composition from nucleotides -20 to +15 with respect to the start. To uncover whether these biases constitute the discriminating information or simply reflect coding constraints, translational starts were randomly searched in eukaryotic, largely non-coding, DNA. These "eukaryotic" starts all have an in-phase AUG or GUG, preceded by a typical Shine-Dalgarno sequence; outside these elements, the initiator region is strikingly rich in A, and poor in C. These biases match those found around real starts, demonstrating that they are indeed part of the initiation signal. Finally, I describe a simple procedure for introducing any DNA fragment in place of the lac operator site on the E. coli chromosome.     

Methionine Sulfoxides on Prion Protein Helix-3 Switch on the α-Fold Destabilization Required for Conversion

Background

The conversion of the cellular prion protein (PrP^C) into the infectious form (PrP^Sc) is the key event in prion induced neurodegenerations. This process is believed to involve a multi-step conformational transition from an α-helical (PrP^C) form to a β-sheet-rich (PrP^Sc) state. In addition to the conformational difference, PrP^Sc exhibits as covalent signature the sulfoxidation of M213. To investigate whether such modification may play a role in the misfolding process we have studied the impact of methionine oxidation on the dynamics and energetics of the HuPrP(125–229) α-fold.

Methodology/Principal Findings

Using molecular dynamics simulation, essential dynamics, correlated motions and signal propagation analysis, we have found that substitution of the sulfur atom of M213 by a sulfoxide group impacts on the stability of the native state increasing the flexibility of regions preceding the site of the modification and perturbing the network of stabilizing interactions. Together, these changes favor the population of alternative states which maybe essential in the productive pathway of the pathogenic conversion. These changes are also observed when the sulfoxidation is placed at M206 and at both, M206 and M213.

Conclusions/Significance

Our results suggest that the sulfoxidation of Helix-3 methionines might be the switch for triggering the initial α-fold destabilization required for the productive pathogenic conversion.     

Novel imaging agents for β-amyloid plaque based on the N-benzoylindole core

We report the synthesis and evaluation of a series of N-benzoylindole derivatives as novel potential imaging agents for β-amyloid plaques. In vitro binding studies using Aβ(1-40) aggregates versus [(125)I]TZDM showed that all these derivatives demonstrated high binding affinities (K(i) values ranged from 8.4 to 121.6 nM). Moreover, two radioiodinated compounds [(125)I]7 and [(125)I]14 were prepared. Autoradiography for [(125)I]14 displayed intense and specific labeling of Aβ plaques in the brain sections of AD model mice (C57, APP/PS1) with low background. In vivo biodistribution in normal mice exhibited sufficient initial brain uptake for imaging (2.19% and 2.00%ID/g at 2 min postinjection for [(125)I]7 and [(125)I]14, respectively). Although additional modifications are necessary to improve brain uptake and clearance from the brain, the N-benzoylindole may be served as a backbone structure to develop novel β-amyloid imaging probes.     

Update on the Search for Miss Waldron’s Red Colobus Monkey

Miss Waldron’s red colobus (Procolobus badius waldroni) has a restricted distribution in eastern Ivory Coast and western Ghana. There have been no confirmed sightings of them since 1978 and surveys carried out from 1993 to the present have yet to reveal any living individual. Since the announcement of the monkey’s probable extinction (Oates et al., 2000), new evidence from forest in the extreme southeast of Ivory Coast suggests that a handful of individuals have remained undetected to this point. I discuss the evidence—a tail, a skin and a photograph—and results of accompanying surveys. Additional surveys of the Ehy Forest are required to confirm the presence of Procolobus badius waldroni and an Action Plan for the conservation of all red colobus across the continent is needed to prevent the disappearance of other taxa.     

Characterization of the lipase immobilized on Mg–Al hydrotalcite for biodiesel

Immobilization of Saccharomyces cerevisiae lipase by physical adsorption on Mg–Al hydrotalcite with a Mg/Al molar ratio of 4.0 led to a markedly improved performance of the enzyme. The immobilized lipase retained activity over wider ranges of temperature and pH than those of the free lipase. The immobilized lipase retained more than 95% relative activity at 50 °C, while the free lipase retained about 88%. The kinetic constants of the immobilized and free lipases were also determined. The apparent activation energies (E_a) of the free and immobilized lipases were estimated to be 6.96 and 2.42 kJ mol^?1, while the apparent inactivation energies (E_d) of free and immobilized lipases were 6.51 and 6.27 kJ mol^?1, respectively. So the stability of the immobilized lipase was higher than that of free lipase. The water content of the oil must be kept below 2.0 wt% and free fatty acid content of the oil must be kept below 3.5 mg KOH g [oil]^?1 in order to get the best conversion. This immobilization method was found to be satisfactory to produce a stable and functioning biocatalyst which could maintain high reactivity for repeating 10 batches with ester conversion above 81.3%.     

Alien futures: What is on the horizon for biological invasions?

Aim

To collect and identify the issues that may affect the future global and local management of biological invasions in the next 20–50 years and provide guidance for the prioritization of actions and policies responding to the management challenges of the future.

Location

Global

Methods

We used an open online survey to poll specialists and stakeholders from around the world as to their opinion on the three most important future issues both globally and at their respective local working level.

Results

The 240 respondents identified 629 global issues that we categorized into topics. We summarized the highest rated topics into five broad thematic areas: (1) environmental change, particularly climate change, (2) the spread of species through trade, (3) public awareness, (4) the development of new technologies to enhance management and (5) the need to strengthen policies. The respondents also identified 596 issues at their respective local working levels. Management, early detection, prevention and funding‐related issues all ranked higher than at the global level. Our global audience of practitioners, policymakers and researchers also elicited topics not identified in horizon scanning exercises led by scientists including potential human health impacts, the need for better risk assessments and legislation, the role of human migration and water management.

Main conclusions

The topic areas identified in this horizon scan provide guidance where future policy priorities for invasive alien species should be set. First, to reduce the magnitude and speed of environmental change and its impacts on biological invasions; second, to restrict the movement of potentially invasive alien species via trade; third, to raise awareness with the general public and empower them to act; and finally, to invest in innovative technologies that can detect and mitigate adverse impacts of introduced species.

     

Dead or gone? Bayesian inference on mortality for the dispersing sex

Estimates of age‐specific mortality are regularly used in ecology, evolution, and conservation research. However, estimating mortality of the dispersing sex, in species where one sex undergoes natal dispersal, is difficult. This is because it is often unclear whether members of the dispersing sex that disappear from monitored areas have died or dispersed. Here, we develop an extension of a multievent model that imputes dispersal state (i.e., died or dispersed) for uncertain records of the dispersing sex as a latent state and estimates age‐specific mortality and dispersal parameters in a Bayesian hierarchical framework. To check the performance of our model, we first conduct a simulation study. We then apply our model to a long‐term data set of African lions. Using these data, we further study how well our model estimates mortality of the dispersing sex by incrementally reducing the level of uncertainty in the records of male lions. We achieve this by taking advantage of an expert's indication on the likely fate of each missing male (i.e., likely died or dispersed). We find that our model produces accurate mortality estimates for simulated data of varying sample sizes and proportions of uncertain male records. From the empirical study, we learned that our model provides similar mortality estimates for different levels of uncertainty in records. However, a sensitivity of the mortality estimates to varying uncertainty is, as can be expected, detectable. We conclude that our model provides a solution to the challenge of estimating mortality of the dispersing sex in species with data deficiency due to natal dispersal. Given the utility of sex‐specific mortality estimates in biological and conservation research, and the virtual ubiquity of sex‐biased dispersal, our model will be useful to a wide variety of applications.     

Atomistic basis for the on–off signaling mechanism in SAM-II riboswitch

Many bacterial genes are controlled by metabolite sensing motifs known as riboswitches, normally located in the 5′ un-translated region of their mRNAs. Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform. Here, we report the results of molecular dynamics simulation studies of the S-adenosylmethionine (SAM)-II riboswitch that is involved in regulating translation in sulfur metabolic pathways in bacteria. We show that the ensemble of conformations of the unbound form of the SAM-II riboswitch is a loose pseudoknot structure that periodically visits conformations similar to the bound form, and the pseudoknot structure is only fully formed upon binding the metabolite, SAM. The rate of forming contacts in the unbound form that are similar to that in the bound form is fast. Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.     

An evolutionary perspective on FoxP2: strictly for the birds?

FoxP2 mutations in humans are associated with a disorder that affects both the comprehension of language and its production, speech. This discovery provided the first opportunity to analyze the genetics of language with molecular and neurobiological tools. The amino acid sequence and the neural expression pattern of FoxP2 are extremely conserved, from reptile to man. This suggests an important role for FoxP2 in vertebrate brains, regardless of whether they support imitative vocal learning or not. Its expression pattern pinpoints neural circuits that might have been crucial for the evolution of speech and language, including the basal ganglia and the cerebellum. Recent studies in songbirds show that during times of song plasticity FoxP2 is upregulated in a striatal region essential for song learning. This suggests that FoxP2 plays important roles both in the development of neural circuits and in the postnatal behaviors they mediate.     

Balancing on the crest – Evidence for disruption of the enteric ganglia via inappropriate lineage segregation and consequences for gastrointestinal function

Normal enteric nervous system (ENS) development relies on numerous factors, including appropriate migration, proliferation, differentiation, and maturation of neural crest (NC) derivatives. Incomplete rostral to caudal migration of enteric neural crest-derived progenitors (ENPs) down the gut is at least partially responsible for the absence of enteric ganglia that is a hallmark feature of Hirschsprung disease (HSCR). The thought that ganglia proximal to aganglionosis are normal has guided surgical procedures for HSCR patients. However, chronic gastrointestinal dysfunction suffered by a subset of patients after surgery as well as studies in HSCR mouse models suggest that aberrant NC segregation and differentiation may be occurring in ganglionated regions of the intestine. Studies in mouse models that possess enteric ganglia throughout the length of the intestine (non-HSCR) have also found that certain genetic alterations affect neural crest lineage balance and interestingly many of these mutants also have functional gastrointestinal (GI) defects. It is possible that many GI disorders can be explained in part by imbalances in NC-derived lineages. Here we review studies evaluating ENS defects in HSCR and non-HSCR mouse models, concluding with clinical implications while highlighting areas requiring further study.     

Is the Iron Gate I reservoir on the Danube River a sink for dissolved silica?

Damming rivers changes sediment and nutrient cycles downstream of a dam in many direct and indirect ways. The Iron Gates I reservoir on the Yugoslavian-Romanian border is the largest impoundment by volume on the Danube River holding 3.2billionm³ of water. Silica retention within the reservoir in the form of diatom frustules was postulated to be as high as 600ktyear^–1 in previous studies using indirect methods. This amount of dissolved silicate was not delivered to the coastal Black Sea, and presumably caused a shift in the phytoplankton community there, and subsequent drastic decline in fishery. We directly quantified the amount of dissolved silicate (DSi) entering and leaving the reservoir for 11 continuous months. The budget based on these data reveals two important facts: (1) only about 4% of incoming DSi was retained in the reservoir; (2) the DSi concentrations were relatively low in the rivers upstream of the reservoir compared to regional and global averages. Thus damming the Danube at the Iron Gates could not have caused the decline in DSi concentrations documented downstream of the impoundment. Rather, this change in DSi must have occurred in the headwaters of the Danube River. Potential reasons include the construction of many dams upstream of the Iron Gates, hydrologic changes resulting in lower groundwater levels, and clogging of the riverbed limiting groundwater–river exchange.     

Central projections of the sensory hairs on the gemma of the ant Diacamma: substrate for behavioural modulation?

In the ant genus Diacamma, all workers eclose from their cocoons with little clublike thoracic appendages, called gemmae. Whether these gemmae are mutilated determines individual behaviour, and ultimately reproductive role, in two of the three species examined. The gemmae are covered with sensory hairs, which probably serve a mechanoreceptive function. The sensory afferents arising from these hairs were stained and traced into the central nervous system (CNS). They feature widely distributed collaterals invading all three thoracic ganglia as well as the suboesophageal and the second abdominal ganglia. The multisegmental arborization pattern of the gemma afferents is very similar to that of wing-hair afferents of other ants (queens and males) or other insects in general. This implies that gemmae and wings are homologous structures. We discuss the morphology of the gemma afferents with respect to their possible involvement in the behavioural changes associated with mutilation. The neuronal processing may be modulated by (1) the decrease of sensory input onto interneurons (suggested by the afferents' extensive arborizations); or (2) by the effect of neuromodulatory substances (suggested by the finding that terminals occur within the cell body rind of the ganglion).     

Could a blood test for PTSD and depression be on the horizon?

ABSTRACT

Introduction: Depression and posttraumatic stress disorder (PTSD) are two complex and debilitating psychiatric disorders that result in poor life and destructive behaviors against self and others. Currently, diagnosis is based on subjective rather than objective determinations leading to misdiagnose and ineffective treatments. Advances in novel neurobiological methods have allowed assessment of promising biomarkers to diagnose depression and PTSD, which offers a new means of appropriately treating patients.

Areas covered: Biomarkers discovery in blood represents a fundamental tool to predict, diagnose, and monitor treatment efficacy in depression and PTSD. The potential role of altered HPA axis, epigenetics, NPY, BDNF, neurosteroid biosynthesis, the endocannabinoid system, and their function as biomarkers for mood disorders is discussed. Insofar, we propose the identification of a biomarker axis to univocally identify and discriminate disorders with large comorbidity and symptoms overlap, so as to provide a base of support for development of targeted treatments. We also weigh in on the feasibility of a future blood test for early diagnosis.

Expert commentary: Potential biomarkers have already been assessed in patients’ blood and need to be further validated through multisite large clinical trial stratification. Another challenge is to assess the relation among several interdependent biomarkers to form an axis that identifies a specific disorder and secures the best-individualized treatment. The future of blood-based tests for PTSD and depression is not only on the horizon but, possibly, already around the corner.