Advances in the Development of Phage-Based Probes for Detection of Bio-Species

Bacteriophages, abbreviated as “phages”, have been developed as emerging nanoprobes for the detection of a wide variety of biological species, such as biomarker molecules and pathogens. Nanosized phages can display a certain length of exogenous peptides of arbitrary sequence or single-chain variable fragments (scFv) of antibodies that specifically bind to the targets of interest, such as animal cells, bacteria, viruses, and protein molecules. Metal nanoparticles generally have unique plasmon resonance effects. Metal nanoparticles such as gold, silver, and magnetism are widely used in the field of visual detection. A phage can be assembled with metal nanoparticles to form an organic–inorganic hybrid probe due to its nanometer-scale size and excellent modifiability. Due to the unique plasmon resonance effect of this composite probe, this technology can be used to visually detect objects of interest under a dark-field microscope. In summary, this review summarizes the recent advances in the development of phage-based probes for ultra-sensitive detection of various bio-species, outlining the advantages and limitations of detection technology of phage-based assays, and highlighting the commonly used editing technologies of phage genomes such as homologous recombination and clustered regularly interspaced palindromic repeats/CRISPR-associated proteins system (CRISPR-Cas). Finally, we discuss the possible scenarios for clinical application of phage-probe-based detection methods.

Transformational Change for People and the Planet: Evaluating Environment and Development – Introduction

The world is facing multiple crises as manifested in runaway climate change, a global pandemic, loss of ecosystems and biological species, and rapidly growing inequality. These are all closely interlinked as recognized in the 2030 Agenda for Sustainable Development. Addressing them will require broad transformational change that encompasses the economy, institutions, and how we interact with the natural environment. This chapter introduces the book that is intended to highlight how evaluation can contribute to such transformations. The chapter first reviews the state of development evaluation. It then briefly introduces the state of the global environment before discussing the implications of this context for evaluation, and how evaluation as a profession and practice must change in order to respond to the challenges of sustainability. The chapter ends by explaining the flow of the book in its four parts that focus on: transformational change, drivers of sustainability, climate change mitigation and adaptation, and evaluation approaches.

Species and speciation.

This chapter discusses two species models, which are diametrically opposed. The first, often called the 'biological species concept', defines species in terms of 'reproductive isolation', convinced that species arise when subsets of a population are split off and remain geographically isolated over evolutionary time. If and when such new species are reunited with their founder population, interbreeding does not occur, or if it does, infertile progeny result. Hence, from the biological species concept, natural selection is a primary agent of change and directly selects for new species. In this sense, species are the direct products of natural selection and they are therefore 'adaptive devices'. When applying this species concept, it has been impossible to separate some sibling species of fruit flies in the genus Bactrocera where distinct morphological species can be similar in molecular analyses of certain DNA sequences, while similar species morphologically are distinct in the same molecular characters. A radically different model, the 'recognition concept of species', relies heavily on a knowledge of species ecology and behaviour, particularly in their natural habitat. The principal points in this concept are given. In contrast to the now-outdated biological species concept that leads one to depend on laboratory-based research to define species, the recognition concept requires workers to undertake extensive field research in the habitat of the taxon under investigation. In translating this approach to research in the insect family Tephritidae, particularly the Dacinae, some 35 years of field surveys have been undertaken throughout the Indian subcontinent, South-east Asia and the South Pacific region. These surveys included trapping using male lure traps and host fruit collections of commercial/edible fruits. The results of this work have included the provision of specimens of almost all known species for morphological descriptions (c.800 species), material for male pheromone chemistry, and data on host fruit relationships and biogeographical studies.

Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha

Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56–33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.

Lithospheric plate tectonics and mass extinctions of biological species

The merging of lithospheric plates and the formation of supercontinents are considered to be the main causes of global species extinctions within the Earth’s biosphere. Under those conditions, the factor of geographic isolation is diminished and interspecies competition is accelerated, allowing for the survival of the best-adapted species. The divergence of lithospheric plates triggers a new spurt of speciation that surpasses the previous one, as it involves the participation of the winning species.

Emergence of uniform linearly-arranged micro-droplets entrapping DNA and living cells through water/water phase-separation

Living cells maintain their lives through self-organization in an environment crowded with a rich variety of biological species. Recently, it was found that micro-droplets containing biomacromolecules, which vary widely in size, are generated accompanied by water/water phase-separation by simple mechanical mixing of an aqueous solution with binary polymers. Here, we report that cell-sized droplets of nearly the same size are generated as a linear array within a glass capillary upon the introduction of a binary polymer solution of polyethylene glycol (PEG) and dextran (DEX). Interestingly, when DNA molecules are added to the polymer solution, stable droplets entrapping DNA molecules are obtained. Similarly, living cells are entrapped spontaneously for the linearly-arranged cell-sized droplets. This simple method for generating micro-droplets entrapping DNA and also living cells is expected to stimulate further study on the self-construction of protocells and micro organoids.

Planar photonic chips with tailored angular transmission for high-contrast-imaging devices

A limitation of standard brightfield microscopy is its low contrast images, especially for thin specimens of weak absorption, and biological species with refractive indices very close in value to that of their surroundings. We demonstrate, using a planar photonic chip with tailored angular transmission as the sample substrate, a standard brightfield microscopy can provide both darkfield and total internal reflection (TIR) microscopy images with one experimental configuration. The image contrast is enhanced without altering the specimens and the microscope configurations. This planar chip consists of several multilayer sections with designed photonic band gaps and a central region with dielectric nanoparticles, which does not require top-down nanofabrication and can be fabricated in a larger scale. The photonic chip eliminates the need for a bulky condenser or special objective to realize darkfield or TIR illumination. Thus, it can work as a miniaturized high-contrast-imaging device for the developments of versatile and compact microscopes.

A lobster-inspired multi-robot control strategy for monitoring non-stationary concentration fields

We propose a new lobster-inspired chemotaxis decentralized control strategy for monitoring a non-stationary concentration field using a team of nonholonomic mobile robots. The task of the team is to locate and trace the movement of the point (or points) with the highest field value (i.e. source), provided that the robots are not aware of the dynamics of the field and can only periodically sample the field at their locations. As an example of the concentration field we consider a population of biological species modeled by a self-organizing multi-agent system with agents acting as individuals of the population in accordance with some flocking rules. The proposed strategy combines the lobsters’ plume localization behavior and flocking mechanisms to efficiently solve the problem even with a small group of robots. Simulations and experimental works on physical unicycle robots are performed to validate the efectiveness of the approach for the cases of non-stationary fields.

The Genealogical Divergence Index Across a Speciation Continuum in Hercules Beetles

The genealogical divergence index (gdi) was developed to aid in molecular species delimitation under the multispecies coalescent model, which has been shown to delimit genetic structures but not necessarily species. Although previous studies have used meta-analyses to show that gdi could be informative for distinguishing taxonomically good species, the biological and evolutionary implications of divergences showing different gdi values have yet to be studied. I showed that an increase in gdi value was correlated with later stages of divergence further along a speciation continuum in an Amazonian Hercules beetle system. Specifically, a gdi value of 0.7 or higher was associated with diverge between biological species that can coexist in geographic proximity while maintaining their evolutionary independence. Divergences between allopatric species that were conventionally given subspecific status, such as geographic taxa that may or may not be morphologically divergent, had gdi values that fell within the species delimitation ambiguous zone (0.2 < gdi < 0.7). However, the results could be drastically affected by the sampling design, i.e., the choice of different geographic populations and the lumping of distinct genetic groups when running the analyses. Different gdi values may prove to be biologically and evolutionarily informative should additional speciation continua from different empirical systems be investigated, and the results obtained may help with objectively delimiting species in the era of integrative taxonomy.