Testing the level of ant activity associated with quorum sensing: an empirical approach leading to the establishment and test of a null-model (response to the comment of Richardson et al.)

In a paper in this journal (Nouvellet et al., 2010), we presented results from experiments on the behaviour of the Pharaoh's ant, Monomorium pharaonis, along with a substantial statistical and theoretical analysis of the results. In a minor part of our paper, we compared our results with the related work of Richardson et al. (2010a). These authors have subsequently commented on our interpretation of their work (Richardson et al., 2011). In this Letter we respond to the comments of Richardson et al. (2011), and give detailed arguments why we stand by our original conclusions.     

Capital and punishment: Resource scarcity increases endorsement of the death penalty

Faced with punishing severe offenders, why do some prefer imprisonment whereas others impose death? Previous research exploring death penalty attitudes has primarily focused on individual and cultural factors. Adopting a functional perspective, we propose that environmental features may also shape our punishment strategies. Individuals are attuned to the availability of resources within their environments. Due to heightened concerns with the costliness of repeated offending, we hypothesize that individuals tend towards elimination-focused punishments during times of perceived scarcity. Using global and United States data sets (studies 1 and 2), we find that indicators of resource scarcity predict the presence of capital punishment. In two experiments (studies 3 and 4), we find that activating concerns about scarcity causes people to increase their endorsement for capital punishment, and this effect is statistically mediated by a reduced willingness to risk repeated offenses. Perceived resource scarcity shapes our punishment preferences, with important policy implications.     

Rolled liverwort mats explain major Prototaxites features: Response to commentaries

In volume 97(2) of the American Journal of Botany (pp. 268-275), we published an article entitled "Structural, physiological, and stable carbon isotopic evidence that the enigmatic Paleozoic fossil Prototaxites formed from rolled liverwort mats". Here, we respond to a letter and a commentary on our article in the present issue, welcoming this opportunity to continue the scientific dialogue about an issue that has long been stimulating and controversial. For the reader's benefit, we first briefly describe the recent scholarly context of our article.     

Control of hemA expression in Rhodobacter sphaeroides 2.4.1: effect of a transposon insertion in the hbdA gene

The common precursor to all tetrapyrroles is 5-aminolevulinic acid (ALA), and in Rhodobacter sphaeroides its formation occurs via the Shemin pathway. ALA synthase activity is encoded by two differentially regulated genes in R. sphaeroides 2.4.1: hemA and hemT. In our investigations of hemA regulation, we applied transposon mutagenesis under aerobic conditions, followed by a selection that identified transposon insertion mutants in which hemA expression is elevated. One of these mutants has been characterized previously (J. Zeilstra-Ryalls and S. Kaplan, J. Bacteriol. 178:985-993, 1996), and here we describe our analysis of a second mutant strain. The transposon inserted into the coding sequences of hbdA, coding for S-(+)-beta-hydroxybutyryl-coenzyme A dehydrogenase and catalyzing an NAD-dependent reaction. We provide evidence that the hbdA gene product participates in polyhydroxybutyrate (PHB) metabolism and, based on our findings, we discuss possibilities as to how defective PHB metabolism might alter the level of hemA expression.     

Encapsulation of Ferritin, Ribosomes, and Ribo-Peptidic Complexes Inside Liposomes: Insights Into the Origin of Metabolism

Here we summarize the main results of our latest investigation on the spontaneous encapsulation of proteins (ferritin) and ribosomes inside lipid vesicles. We show that when vesicles form in a solution containing some macromolecules (even at low concentration), in contrast to the expectations, a few but measurable number of vesicles is able to capture a very high number of solutes, up to 60 times the external concentration. We also show preliminary evidences on the encapsulation of additional solutes (ribo-peptidic complexes, fluorescent proteins and enzymes), and shortly present our current approach aimed at exploiting this phenomenon. In particular, we would like to reveal how the formation of compartments can trigger effective intra-vesicle reactions starting from diluted solutions. Although the mechanistic details for this phenomenon are still missing, we claim that these new evidences are highly relevant for the origin of the first functional cells in primitive times.     

Offshore refuges support higher densities and show slower population declines of wintering Ruddy Turnstones Arenaria interpres: a response

ABSTRACT

In this reply, we confirm that the results of the original paper are robust and that our conclusions were correct: densities of Ruddy Turnstones Arenaria interpres were lower on sites located further from undisturbed refuges. There are two points of learning here: (i) taking the findings of a paper based purely on what is published is normal but there is an unpublished iterative process for analysis that is often hidden from a reader (described here), so we refute that our results were caused by chance; (ii) we published a result based on an incorrect method in the revision process. We hope that other researchers involved in long-term projects involving large and complex datasets can learn from our mistake, as we will endeavour to do.     

A Review of an Ultrafast and Sensitive Bioassay Platform Technology: Microwave-accelerated Metal-enhanced Fluorescence

Since the publication of our first paper on the microwave-accelerated metal-enhanced fluorescence (MAMEF) bioassay platform technology in 2005 (Aslan and Geddes, Anal Chem 77:8057–8067, 2005), we have been repeatedly asked to comment on the advantages of “microwave heating” with plasmonic nanostructures over conventional heating for bioassays by many of our colleagues in the community. We note that one can find a couple of review articles, one by Mingos (Gabriel et al., Chem Soc Rev 27:213–223, 1998) and another by Thostenson and Chou (Manufacturing 30:1055–1071, 1999), summarizing the fundamentals and several applications of microwave processing of chemical compounds and composite materials, respectively. These review articles also present a direct comparison of microwave heating with conventional heating with respect to the processing of materials and microwave-assisted synthesis of chemical compounds. In this review article, we seek to remind the reader of the fundamentals of microwave heating and the interactions of microwaves with chemical and biological materials relevant to our recent work on bioassays, rather than repeating the information provided in the above-mentioned very informative reviews. We also summarize our work on MAMEF-based bioassays where we use plasmonic nanostructures to additionally plasmon-enhance fluorescence signatures.     

Addressing power asymmetries in global health: Imperatives in the wake of the COVID-19 pandemic

Seye Abimbola and co-authors argue for a transformation in global health research and practice in the post-COVID-19 world.

Summary points

• The Coronavirus Disease 2019 (COVID-19) pandemic, the Black Lives Matter and Women in Global Health movements, and ongoing calls to decolonise global health have all created space for uncomfortable but important conversations that reveal serious asymmetries of power and privilege that permeate all aspects of global health.
• In this article, we, a diverse, gender-balanced group of public (global) health researchers and practitioners (most currently living in the so-called global South), outline what we see as imperatives for change in a post-pandemic world.
• At the individual level (including and especially ourselves), we emphasise the need to emancipate and decolonise our own minds (from the colonial conditionings of our education), straddle and use our privilege responsibly (to empower others and avoid elite capture), and build “Southern” networks (to affirm our ownership of global health).
• At the organisational level, we call for global health organisations to practice real diversity and inclusion (in ways that go beyond the cosmetic), to localise their funding decisions (with people on the ground in the driving seat), and to progressively self-decentralise (and so, divest themselves of financial, epistemic, and political power).
• And at both the individual and organisational level, we emphasise the need to hold ourselves, our governments, and global health organisations accountable to these goals, and especially for governance structures and processes that reflect a commitment to real change.
• By putting a spotlight on coloniality and existing inequalities, the COVID-19 pandemic inspires calls for a more equitable world and for a decolonised and decentralised approach to global health research and practice, one that moves beyond tokenistic box ticking about diversity and inclusion into real and accountable commitments to transformative change.

     

Ribbon worm relationships: a phylogeny of the phylum Nemertea

We present the most extensive phylogenetic analysis to date, to our knowledge, of higher-level nemertean relationships, based on sequence data from four different genes (the nuclear genes for nuclear large subunit rRNA (28S rRNA) and histone H3 (H3), and the mitochondrial genes for mitochondrial large subunit rRNA (16S rRNA) and cytochrome c oxidase subunit I (COI)). Well-supported clades are, in general, compatible with earlier, more limited, analyses, and current classification is largely in agreement with our results, although there are some notable exceptions. Bdellonemertea (represented by Malacobdella) is found to be a part of Monostilifera, and Polystilifera is the monophyletic sister group to Monostilifera. Cratenemertidae is the sister group to the remaining monostiliferans (including Malacobdella), a group to which we apply the new name Distromatonemertea. Heteronemertea is monophyletic and forms a clade with Hubrechtella; for this clade we introduce the name Pilidiophora. Finally, Pilidiophora and Hoplonemertea (with Malacobdella) form a monophyletic group, and we introduce the name Neonemertea to refer to this group. Palaeonemertea is found to be non-monophyletic and basal among nemerteans.     

Correction: Helicobacter pylori and gastroduodenal pathology: New threats of the old friend

Since publication of our article (Ahmed and Sechi: Ann Clin Microbiol Antimicrob 2005, 4:1), we have noticed several errors.     

Surgery Issue: Thoracic Aortic Aneurysm: Reading the Enemy’s Playbook

Background: At the Yale University Center for Thoracic Aortic Disease, we have been using our clinical experience and laboratory investigations to shed light on the pathophysiology of thoracic aortic aneurysm (TAA), the clinical behavior of thoracic aortic aneurysm, and the optimal clinical management.     

A new theory of cytotoxic T-lymphocyte memory: implications for HIV treatment

We use simple mathematical models to examine the dynamics of primary and secondary cytotoxic T-lymphocyte (CTL) responses to viral infections. In particular, we are interested in conditions required to resolve the infection and to protect the host upon secondary challenge. While protection against reinfection is only effective in a restricted set of circumstances, we find that resolution of the primary infection requires persistence of CTL precursors (GTLp), as well as a fast rate of activation of the CTLp. Since these are commonly the defining characteristics of CTL memory, we propose that CTL memory may have evolved in order to clear the virus during primary challenge. We show experimental data from lymphocytic choriomeningitis virus infection in mice, supporting our theory on CTL memory. We adapt our models to HIV and find that immune impairment during the primary phase of the infection may result in the failure to establish CTL memory which in turn leads to viral persistence. Based on our models we suggest conceptual treatment regimes which ensure establishment of CTL memory. This would allow the immune response to control HIV in the long term in the absence of continued therapy.     

Grand challenges in organismal biology: The need to develop both theory and resources

This contribution is fifth in a series of articles in Integrative and Comparative Biology that was initiated by Schwenk et al. (2009) and followed by Satterlie et al. (2009), Denny and Helmuth (2009), and Denver et al. (2009). Here, our intent is to be provocative and to stimulate further discourse. Like other contributors we have our own biases, and as it should be clear to the readers, we approach this task as evolutionary biologists, specifically systematists.     

Gonadal steroid enhancement of facial nerve regeneration: Role of heat shock protein 70

Over the past decade, our laboratory has been investigating the now well-established neurotrophic capabilities of gonadal steroids in the context of peripheral nerve injury and repair. The focus of our work has been on the hamster facial motoneuron (FMN) system (Kujawa & Jones, 1995), although we have recently begun to explore two additional motoneuron injury paradigms, the rat sciatic and hamster rubrospinal systems (Kujawa et al., 1993). In this brief review, we will discuss the effects of androgens and estrogens on the regenerative properties and the molecular programming of injured hamster FMN. This will be followed by a discussion of the effects of androgens on the glial response to injury in the facial nucleus. Finally, a working model of the mechanism by which gonadal steroids enhance neuronal reparative processes will be advanced. Our proposed mechanism involves a neuroprotective role for gonadal steroids, in that we hypothesize that exposure to these agents at the time of injury reduces the need for the injured neuron to mount a classical “stress response” involving the production of heat shock protein 70. Finally, a series of future directions for our work will be presented.     

Heuristic Reusable Dynamic Programming: Efficient Updates of Local Sequence Alignment

Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching result between two amino acid sequences, we perform a forward-backward alignment to generate heuristic searching bands which are bounded by a set of suboptimal paths. Given a correctly updated sequence, we initially predict a new score of the alignment path for each contour to select the best candidates among them. Then, we run the Smith-Waterman algorithm in this confined space. Furthermore, our heuristic alignment for an updated sequence shows that it can be further accelerated by using reusable dynamic programming (rDP), our prior work. In this study, we successfully validate "relative node tolerance bound” (RNTB) in the pruned searching space. Furthermore, we improve the computational performance by quantifying the successful RNTB tolerance probability and switch to rDP on perturbation-resilient columns only. In our searching space derived by a threshold value of 90 percent of the optimal alignment score, we find that 98.3 percent of contours contain correctly updated paths. We also find that our method consumes only 25.36 percent of the runtime cost of sparse dynamic programming (sDP) method, and to only 2.55 percent of that of a normal dynamic programming with the Smith-Waterman algorithm.     

“Ecology of fear” in ungulates: Opportunities for improving conservation

Because ungulates are important contributors to ecosystem function, understanding the “ecology of fear” could be important to the conservation of ecosystems. Although studying ungulate ecology of fear is common, knowledge from ungulate systems is highly contested among ecologists. Here, we review the available literature on the ecology of fear in ungulates to generalize our current knowledge and how we can leverage it for conservation. Four general focus areas emerged from the 275 papers included in our literature search (and some papers were included in multiple categories): behavioral responses to predation risk (79%), physiological responses to predation risk (15%), trophic cascades resulting from ungulate responses to predation risk (20%), and manipulation of predation risk (1%). Of papers focused on behavior, 75% were about movement and habitat selection. Studies were biased toward North America (53%), tended to be focused on elk (Cervus canadensis; 29%), and were dominated by gray wolves (40%) or humans (39%) as predators of interest. Emerging literature suggests that we can utilize predation risk for conservation with top‐down (i.e., increasing predation risk) and bottom‐up (i.e., manipulating landscape characteristics to increase risk or risk perception) approaches. It is less clear whether fear‐related changes in physiology have population‐level fitness consequences or cascading effects, which could be fruitful avenues for future research. Conflicting evidence of trait‐mediated trophic cascades might be improved with better replication across systems and accounting for confounding effects of ungulate density. Improving our understanding of mechanisms modulating the nature of trophic cascades likely is most important to ensure desirable conservation outcomes. We recommend future work embrace the complexity of natural systems by attempting to link together the focal areas of study identified herein.     

BNTagger: improved tagging SNP selection using Bayesian networks

Genetic variation analysis holds much promise as a basis for disease-gene association. However, due to the tremendous number of candidate single nucleotide polymorphisms (SNPs), there is a clear need to expedite genotyping by selecting and considering only a subset of all SNPs. This process is known as tagging SNP selection. Several methods for tagging SNP selection have been proposed, and have shown promising results. However, most of them rely on strong assumptions such as prior block-partitioning, bi-allelic SNPs, or a fixed number or location of tagging SNPs. We introduce BNTagger, a new method for tagging SNP selection, based on conditional independence among SNPs. Using the formalism of Bayesian networks (BNs), our system aims to select a subset of independent and highly predictive SNPs. Similar to previous prediction-based methods, we aim to maximize the prediction accuracy of tagging SNPs, but unlike them, we neither fix the number nor the location of predictive tagging SNPs, nor require SNPs to be bi-allelic. In addition, for newly-genotyped samples, BNTagger directly uses genotype data as input, while producing as output haplotype data of all SNPs. Using three public data sets, we compare the prediction performance of our method to that of three state-of-the-art tagging SNP selection methods. The results demonstrate that our method consistently improves upon previous methods in terms of prediction accuracy. Moreover, our method retains its good performance even when a very small number of tagging SNPs are used.     

Ion channels: molecular targets of neuroactive insecticides

Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p′-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); γ-aminobutyric acid (GABA) receptors (cyclodienes, γ-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.