Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals

Metazoans host complex communities of microorganisms that include dinoflagellates, fungi, bacteria, archaea, and viruses. Interactions among members of these complex assemblages allow hosts to adjust their physiology and metabolism to cope with environmental variation and occupy different habitats. Here, using reciprocal transplantation across depths, we studied adaptive divergence in the Caribbean corals Orbicella annularis and O. franksi. When transplanted from deep to shallow, O. franksi experienced fast photoacclimation, low mortality, and maintained a consistent bacterial community. In contrast, O. annularis experienced higher mortality, and limited photoacclimation when transplanted from shallow to deep. The photophysiological collapse of O. annularis in the deep environment was associated with an increased microbiome variability and reduction of some bacterial taxa. Differences in the symbiotic algal community were more pronounced between coral species than between depths. Our study suggests that these sibling species are adapted to distinctive light environments partially driven by the algae photoacclimation capacity and the microbiome robustness, highlighting the importance of niche specialization in symbiotic corals for the maintenance of species diversity. Our findings have implications for the management of these threatened Caribbean corals and the effectiveness of coral reef restoration efforts.

Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System

In vitro fermentors that can host complex gut microbial communities are promising tools to investigate the dynamics of human gut microbiota. In this work, using an automated in vitro gut fermentor consisting of different colon compartments, we investigated the adaptation dynamics of two different human fecal microbial communities over 22 and 31 days.

Single cells and transposable element heterogeneity in stem cells and development

Recent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented detail. However, several cellular aspects are currently underutilized in single cell studies. One aspect is the expression and activity of transposable elements (TEs). TEs are selfish sequences of DNA that can replicate, and have been wildly successful in colonizing genomes. However, most TEs are mutated, fragmentary and incapable of transposition, yet they are actively bound by multiple transcription factors, host complex patterns of chromatin modifications, and are expressed in mRNAs as part of the transcriptome in both normal and diseased states. The contribution of TEs to development and cellular function remains unclear, and the routine inclusion of TEs in single cell sequencing analyses will potentially lead to insight into stem cells, development and human disease.

Linguistic Representation and Processing of Copredication

This thesis addresses the lexical and psycholinguistic properties of copredication. In particular, it explores its acceptability, frequency, cross-linguistic and electrophysiological features. It proposes a general parsing bias to account for novel acceptability data, through which Complex-Simple predicate orderings are degraded across distinct nominal types relative to the reverse order. This bias, Incremental Semantic Complexity, states that the parser seeks to process linguistic representations in incremental stages of semantic complexity. English and Italian acceptability data are presented which demonstrate that predicate order preferences are based not on sense dominance but rather sense complexity. Initial evidence is presented indicating that pragmatic factors centred on coherence relations can impact copredication acceptability when such copredications host complex (but not simple) predicates. The real-time processing and electrophysiological properties of copredication are also presented, which serve to replicate and ground the acceptability dynamics presented in the thesis.

A Design Guide for Usable Web APIs

Cloud computing trends such as Software as a Service (SaaS) enable providers to host complex applications over the Internet, making them available to external consumers through an Application Programming Interface (API). The success of a SaaS, and in some sense any distributed system, is greatly influenced by its API. Highly usable APIs improve the efficiency of the development process and its quality, ensuring that programmers continue to appreciate other aspects of the API while increasing their productivity. Different studies state that the design phase within the development process of an API is the most appropriate to address usability issues. Therefore, usability should be considered as an explicit criterion in the design of an API. In this paper, we propose a design guide for web APIs with an emphasis on usability, using the best practices of usable web APIs design. Our design guide is based on an adaptation of the design science research methodology (DSRM), and it is complemented with a systematic literature review and gray literature analysis concerning methods, techniques, and tools used to develop usable APIs.

Sonography of Knee Effusion

Objective: A review of the anatomy of the synovial recesses of the knee is important to better understand the different effusion presentations, update the diagnosis criteria of knee effusion based on the measured synovial recesses and discuss the differentiation of some effused recesses from other lesions around the knee. Method: This review focuses on the anatomy of the synovial recesses of the knee and classifies them into three groups (anterior, parameniscal, and posterior recesses), as well as provides an overview on the etiology of knee effusion, its sonographic detection, and diagnosis criteria. Results: Knee effusion is a very common pathological finding in sonography of the knee. The unique joint structure of the knee provides the possibility to host complex synovial recesses. Fluid in some of the synovial recesses is valuable for the diagnosis of knee effusion, while in certain situations, some recesses may impose diagnostic uncertainty. Knowledge of these synovial recesses is essential to avoid diagnostic pitfalls. Conclusion: This review provides an important discussion of the differentiation of some recesses effusions from other lesions around the knee.

Skyrmion lattice with a giant topological Hall effect in a frustrated triangular-lattice magnet

Geometrically frustrated magnets can host complex spin textures, leading to unconventional electromagnetic responses. Magnetic frustration may also promote topologically nontrivial spin states such as magnetic skyrmions. Experimentally, however, skyrmions have largely been observed in noncentrosymmetric lattice structures or interfacial symmetry-breaking heterostructures. Here, we report the emergence of a Bloch-type skyrmion state in the frustrated centrosymmetric triangular-lattice magnet Gd2PdSi3. We observed a giant topological Hall response, indicating a field-induced skyrmion phase, which is further corroborated by the observation of in-plane spin modulation probed by resonant x-ray scattering. Our results may lead to further discoveries of emergent electrodynamics in magnetically frustrated centrosymmetric materials.

Phytoclimatic mapping of exoplanets

The concept of exoplanetary habitability is evolving. The driving force is a desire to define the biological potential of planets and identify which can host complex and possibly intelligent life. To assess this in a meaningful manner, climate models need to be applied to realistic surfaces. However, the vast majority of climate models are developed using generic aquaplanet, or swamp planet, scenarios that provide uniform, surface frictional coefficients. However, aside from planets with largely uniform oceans, these models are not obviously useful when it comes to understanding the impact of climate on biodiversity. Here, we show that contrary to expectation, the aquaplanet models can be directly applied to planets with a variety of land areas, with little need for modification. Using this premise, this paper provides a simple mathematical framework that may be applied to more complex planetary surfaces and identifies the majority of the climate-model components that are needed to accurately determine the biological potential of habitable exoplanets. As a proof-of-concept, an available climate model for Proxima b is used to determine its biological potential, given a suitable atmosphere.

Morphological characterization of virus-like particles in coral reef sponges

Marine sponges host complex microbial consortia that vary in their abundance, diversity and stability amongst host species. While our understanding of sponge-microbe interactions has dramatically increased over the past decade, little is known about how sponges and their microbial symbionts interact with viruses, the most abundant entities in the ocean. In this study, we employed three transmission electron microscopy (TEM) preparation methods to provide the first comprehensive morphological assessment of sponge-associated viruses. The combined approaches revealed 50 different morphologies of viral-like particles (VLPs) represented across the different sponge species. VLPs were visualized within sponge cells, within the sponge extracellular mesohyl matrix, on the sponge ectoderm and within sponge-associated microbes. Non-enveloped, non-tailed icosahedral VLPs were the most commonly observed morphotypes, although tailed bacteriophage, brick-shaped, geminate and filamentous VLPs were also detected. Visualization of sponge-associated viruses using TEM has confirmed that sponges harbor not only diverse communities of microorganisms but also diverse communities of viruses.