Mixing and transport by ciliary carpets: a numerical study

We use a 3D computational model to study the fluid transport and mixing due to the beating of an infinite array of cilia. In accord with recent experiments, we observe two distinct regions: a fluid transport region above the cilia and a fluid mixing region below the cilia tip. The metachronal wave due to phase differences between neighboring cilia is known to enhance the fluid transport above the ciliary tip. In this work, we show that the metachronal wave also enhances the mixing rates in the sub-ciliary region, often simultaneously with the flow rate enhancement. Our results suggest that this simultaneous enhancement in transport and mixing is due to an enhancement in shear flow. As the flow above the cilia increases, shear rate in the fluid increases and such shear enhances stretching, which is an essential ingredient for mixing. Estimates of the mixing time scale indicate that, compared to diffusion, the mixing due to the cilia beat may be significant and sometimes dominates chemical diffusion.Comment: submitted to Journal of Fluid Mechanic

Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans(1,2). Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host(3-6). We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)(7,8) and has a genomic repertoire similar to that of rickettsial parasites(9,10), but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations(11-13). This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter

Functional morphology of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae), a bacterially luminous coral reef fish

Previous studies of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae) identified a ventral light organ, reflector, lens, duct, and a ventral diffuser extending from the throat to the caudal peduncle. The control and function of luminescence in this and other species of Siphamia , however, have not been defined. Morphological examination of fresh and preserved specimens identified additional components of the luminescence system involved in control and ventral emission of luminescence, including a retractable shutter over the ventral face of the light organ, contiguity of the ventral diffuser from the caudal peduncle to near the chin, and transparency of the bones and other tissues of the lower jaw. The shutter halves retract laterally, allowing the ventral release of light, and relax medially, blocking ventral light emission; topical application of norepinephrine to the exposed light organ resulted in retraction of the shutter halves, which suggests that operation of the shutter is under neuromuscular control. The extension of the diffuser to near the chin and transparency of the lower jaw allow a uniform emission of luminescence over the entire ventrum of the fish. The live aquarium‐held fish were found to readily and consistently display ventral luminescence. At twilight, the fish left the protective association with their longspine sea urchin, Diadema setosum , and began to emit ventral luminescence and to feed on zooplankton. Ventral luminescence illuminated a zone below and around the fish, which typically swam close to the substrate. Shortly after complete darkness, the fish stopped feeding and emitting luminescence. These observations suggest that S. versicolor uses ventral luminescence to attract and feed on zooplankton from the reef benthos at twilight. Ventral luminescence may allow S. versicolor to exploit for feeding the gap at twilight in the presence of potential predators as the reef transitions from diurnally active to nocturnally active organisms. J. Morphol., 2011. © 2011 Wiley‐Liss, IncPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86998/1/10956_ftp.pd

In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host- Symbiont Interaction

Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. <i>Spiroplasma poulsonii</i> is a maternally transmitted bacterial endosymbiont that is naturally associated with several <i>Drosophila</i> species. <i>S. poulsonii</i> strongly affects its host's physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic <i>Spiroplasma in vitro</i> have failed so far. Here, we developed a method to sustain the <i>in vitro</i> culture of <i>S. poulsonii</i> by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic <i>Spiroplasma</i> species. Last, by comparing the transcriptome of the <i>in vitro</i> culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic <i>Spiroplasma</i> and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners. <b>IMPORTANCE</b> The discovery of insect bacterial endosymbionts (maternally transmitted bacteria) has revolutionized the study of insects, suggesting novel strategies for their control. Most endosymbionts are strongly dependent on their host to survive, making them uncultivable in artificial systems and genetically intractable. <i>Spiroplasma poulsonii</i> is an endosymbiont of <i>Drosophila</i> that affects host metabolism, reproduction, and defense against parasites. By providing the first reliable culture medium that allows a long-lasting <i>in vitro</i> culture of <i>Spiroplasma</i> and by elucidating its complete genome, this work lays the foundation for the development of genetic engineering tools to dissect endosymbiosis with two partners amenable to molecular study. Furthermore, the optimization method that we describe can be used on other yet uncultivable symbionts, opening new technical opportunities in the field of host-microbes interactions

The Drosophila melanogaster gut microbiota provisions thiamine to its host

The microbiota of Drosophila melanogaster has a substantial impact on host physiology and nutrition. Some effects may involve vitamin provisioning, but the relationships between microbe-derived vitamins, diet, and host health remain to be established systematically. We explored the contribution of microbiota in supplying sufficient dietary thiamine (vitamin B1) to support D. melanogaster at different stages of its life cycle. Using chemically defined diets with different levels of available thiamine, we found that the interaction of thiamine concentration and microbiota did not affect the longevity of adult D. melanogaster Likewise, this interplay did not have an impact on egg production. However, we determined that thiamine availability has a large impact on offspring development, as axenic offspring were unable to develop on a thiamine-free diet. Offspring survived on the diet only when the microbiota was present or added back, demonstrating that the microbiota was able to provide enough thiamine to support host development. Through gnotobiotic studies, we determined that Acetobacter pomorum, a common member of the microbiota, was able to rescue development of larvae raised on the no-thiamine diet. Further, it was the only microbiota member that produced measurable amounts of thiamine when grown on the thiamine-free fly medium. Its close relative Acetobacter pasteurianus also rescued larvae; however, a thiamine auxotrophic mutant strain was unable to support larval growth and development. The results demonstrate that the D. melanogaster microbiota functions to provision thiamine to its host in a low-thiamine environment. Importance: There has been a long-standing assumption that the microbiota of animals provides their hosts with essential B vitamins; however, there is not a wealth of empirical evidence supporting this idea, especially for vitamin B1 (thiamine). To determine whether this assumption is true, we used Drosophila melanogaster and chemically defined diets with different thiamine concentrations as a model. We found that the microbiota does provide thiamine to its host, enough to allow the development of flies on a thiamine-free diet. The power of the Drosophila-microbiota system allowed us to determine that one microbiota member in particular, Acetobacter pomorum, is responsible for the thiamine provisioning. Thereby, our study verifies this long-standing hypothesis. Finally, the methods used in this work are applicable for interrogating the underpinnings of other aspects of the tripartite interaction between diet, host, and microbiota

Opinion: Why science needs philosophy

International audienc

Why science needs philosophy

\textgreater A knowledge of the historic and philosophical background gives that kind of independence from prejudices of his generation from which most scientists are suffering. This independence created by philosophical insight is—in my opinion—the mark of distinction between a mere artisan or specialist and a real seeker after truth. \textgreater \textgreater Albert Einstein, Letter to Robert Thornton, 1944 Despite the tight historical links between science and philosophy, present-day scientists often perceive philosophy as completely different from, and even antagonistic to, science. We argue here that, to the contrary, philosophy can have an important and productive impact on science. Despite the tight historical links between science and philosophy, hearkening back to Plato, Aristotle, and others (here evoked with Raphael’s famous School of Athens), present-day scientists often perceive philosophy as completely different from, and even antagonistic to, science. To the contrary, we believe philosophy can have an important and productive impact on science. Image credit: Shutterstock.com/Isogood_patrick. We illustrate our point with three examples taken from various fields of the contemporary life sciences. Each bears on cutting-edge scientific research, and each has been explicitly acknowledged by practicing researchers as a useful contribution to science. These and other examples show that philosophy’s contribution can take at least four forms: the clarification of scientific concepts, the critical assessment of scientific assumptions or methods, the formulation of new concepts and theories, and the fostering of dialogue between different sciences, as well as between science and society. ### Conceptual Clarification and Stem Cells. First, philosophy offers conceptual clarification. Conceptual clarifications not only improve the precision and utility of scientific terms but also lead to novel experimental investigations because the choice of a given conceptual framework strongly constrains how experiments are conceived. The definition of stem cells is a prime example. Philosophy has a long tradition of investigating properties, and the tools in use in this tradition

Vibrio fischeri -derived outer membrane vesicles trigger host development: OMV deliver signals in the squid/vibrio symbiosis

Outer membrane vesicles (OMV) are critical elements in many host-cell/microbe interactions. Previous studies of the symbiotic association between Euprymna scolopes and Vibrio fischeri had shown that, within 12 h of colonizing crypts deep within the squid’s light organ, the symbionts trigger an irreversible program of tissue development in the host. Here, we report that OMV produced by V. fischeri are powerful contributors to this process. The first detectable host response to the OMV is an increased trafficking of macrophage-like cells called hemocytes into surface epithelial tissues. We showed that exposing the squid to other Vibrio species fails to induce this trafficking; however, addition of a high concentration of their OMV, which can diffuse into the crypts, does. We also provide evidence that tracheal cytotoxin (TCT) release by the symbionts, which can induce hemocyte trafficking, is not part of the OMV cargo, suggesting two distinct mechanisms to induce the same morphogenesis event. By manipulating the timing and localization of OMV signal delivery, we showed that hemocyte trafficking is fully induced only when V. fischeri, the sole species able to reach and grow in the crypts, succeeds in establishing a sustained colonization. Further, our data suggest that the host detection of OMV serves as a symbiotic checkpoint prior to inducing irreversible morphogenesis