Tandem Recruitment and Foraging in the Ponerine Ant <Emphasis Type="Italic">Pachycondyla harpax</Emphasis> (Fabricius)

Tandem running is a common recruitment strategy in ant species with small colony sizes. During a tandem run, an informed leader guides a usually naïve nestmate to a food source or a nest site. Some species perform tandem runs only during house hunting, suggesting that tandem running does not always improve foraging success in species known to use tandem running as a recruitment strategy, but more natural history information on tandem running under natural conditions is needed to better understand the adaptive significance of tandem recruitment in foraging. Studying wild colonies in Brazil, we for the first time describe tandem running in the ponerine ant Pachycondyla harpax (Fabricius). We asked if foragers perform tandem runs to carbohydrate- (honey) and protein-rich (cheese) food items. Furthermore, we tested whether the speed and success rate of tandem runs depend on the foraging distance. Foragers performed tandem runs to both carbohydrate food sources and protein-rich food items that exceed a certain size. The probability to perform a tandem run and the travelling speed increase with increasing foraging distances, which could help colonies monopolize more distant food sources in a competitive environment. Guiding a recruit to a food source is costly for leaders as ants are ~66% faster when travelling alone. If tandem runs break up (~23% of all tandem runs), followers do not usually discover the food source on their own but return to the nest. Our results show that tandem running to food sources is common in P. harpax, but that foragers modify their behaviour according to the type of food and its distance from the nest. Competition with other ants was intense and we discuss how tandem running in P. harpax might help colonies to build-up a critical number of ants at large food items that can then defend the food source against competitors.     

Theories and Major Hypotheses in Ethnobotany

Ethnobotany has evolved from a discipline that largely documented the diversity of plant use by local people to one focused on understanding how and why people select plants for a wide range of uses. This progress has been in response to a repeated call for theory-inspired and hypothesis-driven research to improve the rigor of the discipline. Despite improvements, recent ethnobotanical research has overemphasized the use of quantitative ethnobotany indices and statistical methods borrowed from ecology, yet underemphasized the development and integration of a strong theoretical foundation. To advance the field of ethnobotany as a hypothesis-driven, theoretically inspired discipline, it is important to first synthesize the existing theoretical lines of research. We review and discuss 17 major theories and hypotheses in ethnobotany that can be used as a starting point for developing research questions that advance our understanding of people–plant interactions. For each theory or major hypothesis, we identify its primary predictions and testable hypotheses and then discuss how these predictions have been tested. Developing research to test these predictions will make significant contributions to the field of ethnobotany and create the critical mass of primary literature necessary to develop meta-analyses and to advance new theories in ethnobotany.     

Mex-3C研究新进展：结合RNA的泛素E3连接酶与染色体不稳定性抑制基因

Mex-3C蛋白（又称RKHD2）具备2个串联重复的KH结构域和1个环指结构域,具备结合RNA的能力,同时也是泛素E3连接酶家族的一员.它可以诱导某些mRNA降解,并且这一过程可以被一种去泛素化酶USP7阻断,据此产生了结合RNA的泛素连接酶的概念并暗示泛素化可能与mRNA降解之间存在某种联系. Mex-3C可能通过利用该特性参与调节某些生理功能.另一方面,结直肠癌细胞MEX3C基因缺陷可以导致染色体不稳定性的产生,由此提出了染色体不稳定性抑制基因的观点.DNA复制应激被证实介导了两者之间的相互作用.本文将从这两个新概念出发介绍Mex-3C现有的研究进展,并指出后续的研究方向.     

Informatics for protein identification by mass spectrometry

High throughput protein analysis (i.e., proteomics) first became possible when sensitive peptide mass mapping techniques were developed, thereby allowing for the possibility of identifying and cataloging most 2D gel electrophoresis spots. Shortly thereafter a few groups pioneered the idea of identifying proteins by using peptide tandem mass spectra to search protein sequence databases. Hence, it became possible to identify proteins from very complex mixtures. One drawback to these latter techniques is that it is not entirely straightforward to make matches using tandem mass spectra of peptides that are modified or have sequences that differ slightly from what is present in the sequence database that is being searched. This has been part of the motivation behind automated de novo sequencing programs that attempt to derive a peptide sequence regardless of its presence in a sequence database. The sequence candidates thus generated are then subjected to homology-based database search programs (e.g., BLAST or FASTA). These homology search programs, however, were not developed with mass spectrometry in mind, and it became necessary to make minor modifications such that mass spectrometric ambiguities can be taken into account when comparing query and database sequences. Finally, this review will discuss the important issue of validating protein identifications. All of the search programs will produce a top ranked answer; however, only the credulous are willing to accept them carte blanche.     

The struggle for life of the genome's selfish architects

Abstract  

Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome. Since Darwin's theory of evolution, and the progress of molecular biology, transposable elements may be the discovery that has most influenced our vision of (genome) evolution. In this review, we provide a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome. Numerous examples of these interactions are provided, first from the standpoint of the genome, and then from that of the transposable elements. We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution.     

Homosexual tandem running as selfish herd in Reticulitermes speratus: novel antipredatory behavior in termites.

We investigated the predator avoidance mechanism of post-swarming alates of the lower subterranean termite, Reticulitermes speratus Kolbe. In some lower termites, homosexual tandem running is observed in addition to ordinary heterosexual tandem running. An experiment designed to compare the risk of predation by a termite-hunting ant, Brachyponera chinensis Emery, showed that homosexual tandem running reduced the predation risk until termites encounter the opposite sex. Since an individual ant cannot capture two dealates at once, one of the two dealates forming a tandem can escape while the ant captures its partner. Therefore, the "post-encounter risk" of individuals running in tandem was lower than that of single individuals. The "encounter risk" with predatory ants was also examined using a mathematical model considering the increased detectability of the predator due to enhanced size of the prey unit. It was suggested that tandem running reduces the predation risk of both participants, even when the enhanced encounter risk was taken into account. In males, competition for the back position was often observed, and consequently, the male at the back was always larger than the male in front. When a male-male tandem encountered a female, the back male won the female more often than the front male. This result suggested that male-male tandem running should result in selection pressure in favor of vigorous males. In conclusion, tandem running decreases the individual predation risk through the dilution effect, and it also plays a role as a mechanism of indirect sexual selection.     

Microbiology in the post-genomic era

Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology.     

Understanding Youth Development From the Practitioner's Point of View: A Call for Research on Effective Practice

This article calls for research on the expertise of youth development practitioners. We argue for studies focused on understanding youth practice from practitioners' points of view—as they experience and enact it—with the aim of contributing findings and frameworks that are helpful to their work and learning. To improve youth programs, first, it is essential to better understand the challenges frontline staff face in their work. We review evidence showing that running a program and facilitating youth development is more challenging and multidimensional than is generally appreciated. Second, it is essential to understand the strategies effective practitioners employ to address these challenges. Studies indicate that the expertise of frontline staff is central to program impact; we review findings suggesting the diverse, contextually-attuned skills this expertise entails. Case studies in three domains of decision-making (designing programs, youth's motivation, and ethical dilemmas) are used to provide a vision for this research.     

A review of intensive mode of delivery and science subjects in Australian universities

One response to the global trend of increasing rates of student participation in tertiary education has been for universities to increase the number of intensive mode of delivery subjects available. This phenomenon extends to science subjects. Embarking on offering an undergraduate science subject in intensive mode for the first time at the Australian case example university, it was essential to first learn about good pedagogical design and practice from other educational organisations. To achieve this, a website audit of Australian universities was undertaken in tandem with a critical review of the Australian and international literature on intensive mode of delivery. While it was found that a majority of Australian universities offer science subjects in intensive mode, these subjects were primarily at the postgraduate level of study. The literature focusing on intensive mode in science was minimal. It revealed definitional ambiguity and conceptual non-uniformity as well as a range of positive, negative and inconclusive results in relation to the academic and ‘real-world’ outcomes of intensive mode. This review identifies a need for evidenced-based empirical research into the pedagogy around intensive mode for undergraduate science subjects.     

A review of insect stem cell types

Insect stem cells have been described from both embryonic and adult tissues from a diversity of insect species, although much of the focus in insect stem cell research has been on Drosophila. Insects are a vast and diverse group and it is surprising that a critical aspect of their development like stem cells has not received more attention. In this review we discuss the current state of knowledge of insect stem cell types. We examine what stem cell types have been identified from insects, and briefly discuss what is known about their regulation.     

A trade‐off between antipredatory behavior and pairing competition produced by male‑male tandem running in three Reticulitermes species

Due to the omnipresent risk of predation, termites have evolved many antipredatory behaviors. The two related species Reticulitermes speratus and R. chinensis have been demonstrated to use homosexual tandem running to decrease individual predation risk after shedding their wings. In this study, we tested risk of predation in the termite R. flaviceps, which is distantly related to the above two species. We determined that homosexual tandem running also led to low individual predation risk in dealates of R. flaviceps. Moreover, by combining a predation model with a competition model, we observed a typical trade‐off phenomenon between antipredatory behavior and pairing competition produced by male?male tandem running in the above three Reticulitermes species. Our results indicated that male?male tandem running could effectively protect disadvantaged individuals from being caught, but disadvantaged individuals would be easily eliminated in pairing competition after male?male tandem running, suggesting that male?male tandem running can promote population evolution in termites by repeatedly removing the relatively inferior male individuals.     

Rethinking the role of theory in exploratory experimentation

To explain their role in discovery and contrast them with theory-driven research, philosophers of science have characterized exploratory experiments in terms of what they lack: namely, that they lack direction from what have been called “local theories” of the target system or object under investigation. I argue that this is incorrect: it’s not whether or not there is direction from a local theory that matters, but instead how such a theory is used to direct an experiment that matters. Appealing to contemporary exploratory experiments that involve the use of experimental techniques—specifically, examples where scientists explore the interaction of neural activity and human behavior by magnetically stimulating brains—I argue that local theories of a target system can inform auxiliary hypotheses in exploratory experiments, which direct these experiments. These examples illustrate how local theories can direct the exploration of target systems where researchers do not aim to evaluate these theories.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

Opsin gene duplication and divergence in ray-finned fish

Opsin gene sequences were first reported in the 1980s. The goal of that research was to test the hypothesis that human opsins were members of a single gene family and that variation in human color vision was mediated by mutations in these genes. While the new data supported both hypotheses, the greatest contribution of this work was, arguably, that it provided the data necessary for PCR-based surveys in a diversity of other species. Such studies, and recent whole genome sequencing projects, have uncovered exceptionally large opsin gene repertoires in ray-finned fishes (taxon, Actinopterygii). Guppies and zebrafish, for example, have 10 visual opsin genes each. Here we review the duplication and divergence events that have generated these gene collections. Phylogenetic analyses revealed that large opsin gene repertories in fish have been generated by gene duplication and divergence events that span the age of the ray-finned fishes. Data from whole genome sequencing projects and from large-insert clones show that tandem duplication is the primary mode of opsin gene family expansion in fishes. In some instances gene conversion between tandem duplicates has obscured evolutionary relationships among genes and generated unique key-site haplotypes. We mapped amino acid substitutions at so-called key-sites onto phylogenies and this exposed many examples of convergence. We found that dN/dS values were higher on the branches of our trees that followed gene duplication than on branches that followed speciation events, suggesting that duplication relaxes constraints on opsin sequence evolution. Though the focus of the review is opsin sequence evolution, we also note that there are few clear connections between opsin gene repertoires and variation in spectral environment, morphological traits, or life history traits.     

Speed versus accuracy in decision-making ants: expediting politics and policy implementation

Compromises between speed and accuracy are seemingly inevitable in decision-making when accuracy depends on time-consuming information gathering. In collective decision-making, such compromises are especially likely because information is shared to determine corporate policy. This political process will also take time. Speed–accuracy trade-offs occur among house-hunting rock ants, Temnothorax albipennis. A key aspect of their decision-making is quorum sensing in a potential new nest. Finding a sufficient number of nest-mates, i.e. a quorum threshold (QT), in a potential nest site indicates that many ants find it suitable. Quorum sensing collates information. However, the QT is also used as a switch, from recruitment of nest-mates to their new home by slow tandem running, to recruitment by carrying, which is three times faster. Although tandem running is slow, it effectively enables one successful ant to lead and teach another the route between the nests. Tandem running creates positive feedback; more and more ants are shown the way, as tandem followers become, in turn, tandem leaders. The resulting corps of trained ants can then quickly carry their nest-mates; but carried ants do not learn the route. Therefore, the QT seems to set both the amount of information gathered and the speed of the emigration. Low QTs might cause more errors and a slower emigration—the worst possible outcome. This possible paradox of quick decisions leading to slow implementation might be resolved if the ants could deploy another positive-feedback recruitment process when they have used a low QT. Reverse tandem runs occur after carrying has begun and lead ants back from the new nest to the old one. Here we show experimentally that reverse tandem runs can bring lost scouts into an active role in emigrations and can help to maintain high-speed emigrations. Thus, in rock ants, although quick decision-making and rapid implementation of choices are initially in opposition, a third recruitment method can restore rapid implementation after a snap decision. This work reveals a principle of widespread importance: the dynamics of collective decision-making (i.e. the politics) and the dynamics of policy implementation are sometimes intertwined, and only by analysing the mechanisms of both can we understand certain forms of adaptive organization.     

Taking the Gaia hypothesis at face value

The interest in understanding the climate-life system that has fostered the Gaia hypothesis (GH) has resulted in multiple explanatory theories, making its status unclear and controversial. This work seeks to bring some clarity to the debates surrounding the GH with the aim to make it amenable to scientific scrutiny. We discuss what it means to take the GH at face value and its implications for a potential research programme we call ‘functional climatology’.     

Interdisciplinary integration in biology? An overview

Philosophical theories about reduction and integration in science are at variance with what is happenign in science. A realistic approach to science show that possibilities for reduction and integration are limited. The classical ideal of a unified science has since long been rejected in philosophy. But the current emphasis on interdisciplinary integration in philosophy and in science shows that it survives in a different guise. It is necessary to redress the balance, specifically in biology. Methodological analysis shows that many of the grand interdisciplinary theories involving biology actually represent pseudo-integration covered up by inappropriate, overgeneral concepts. Integrationism is not bad, but it must be kept within reasonable bounds. If the present analysis is appropriate, there will have to be fundamental changes in research strategy both in science and in the philosophy of science.     

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.     

An invitation to ecological economics

The emerging interdisciplinary field of ecological economics should be a recognized research priority. Only through a combination of sound ecology and good economics can we hope to manage our exploitation of the biosphere in a manner that is both sustainable and efficient. This article is an invitation to ecologists to use economic tools and to participate in ecological economic debate. To this end, we review basic ecological economic concepts and discuss how the field has arisen, what benefits it offers, and what challenges it must overcome.