Thematic Review Series: Lysophospholipids and their Receptors: Autotaxin: structure-function and signaling

Autotaxin (ATX), or ecto-nucleotide pyrophosphatase/phosphodiesterase-2, is a secreted lysophospholipase D (lysoPLD) that hydrolyzes extracellular lysophospholipids into the lipid mediator lysophosphatidic acid (LPA), a ligand for specific G protein-coupled receptors. ATX-LPA signaling is essential for development and has been implicated in a great diversity of (patho)physiological processes, ranging from lymphocyte homing to tumor progression. Structural and functional studies have revealed what makes ATX a unique lysoPLD, and how secreted ATX binds to its target cells. The ATX catalytic domain shows a characteristic bimetallic active site followed by a shallow binding groove that can accommodate nucleotides as well as the glycerol moiety of lysophospholipids, and by a deep lipid-binding pocket. In addition, the catalytic domain has an open tunnel of unknown function adjacent to the active site. Here, we discuss our current understanding of ATX structure-function relationships and signaling mechanisms, and how ATX isoforms use distinct mechanisms to target LPA production to the plasma membrane, notably binding to integrins and heparan sulfate proteoglycans. We also briefly discuss the development of drug-like inhibitors of ATX.     

Retinol and retinyl esters: biochemistry and physiology: Thematic Review Series: Fat-Soluble Vitamins: Vitamin A

By definition, a vitamin is a substance that must be obtained regularly from the diet. Vitamin A must be acquired from the diet, but unlike most vitamins, it can also be stored within the body in relatively high levels. For humans living in developed nations or animals living in present-day vivariums, stored vitamin A concentrations can become relatively high, reaching levels that can protect against the adverse effects of insufficient vitamin A dietary intake for six months, or even much longer. The ability to accumulate vitamin A stores lessens the need for routinely consuming vitamin A in the diet, and this provides a selective advantage to the organism. The molecular processes that underlie this selective advantage include efficient mechanisms to acquire vitamin A from the diet, efficient and overlapping mechanisms for the transport of vitamin A in the circulation, a specific mechanism allowing for vitamin A storage, and a mechanism for mobilizing vitamin A from these stores in response to tissue needs. These processes are considered in this review.     

Hormone interactions and regulation of PsPK2::GUS compared with DR5::GUS and PID::GUS in Arabidopsis thaliana

The putative pea PINOID homolog, PsPK2, is expressed in all growing plant parts and is positively regulated by auxin, gibberellin, and cytokinin. Here, we studied hormonal regulation of PsPK2::GUS expression compared with DR5::GUS and PID::GUS in Arabidopsis. PsPK2::GUS, DR5::GUS, and PID::GUS expression in Arabidopsis shoots is mainly localized in the stipules, hydathodes, veins, developing leaves, and cotyledons. Unlike DR5::GUS, PsPK2::GUS, and PID::GUS are weakly expressed in root tips. Both DR5::GUS and PsPK2::GUS are induced by different auxins and are more sensitive to methyl indole acetic acid, 4-chloro-indole acetic acid, and α-naphthalene acetic acid than others. GA(3) has no significant effect on GUS activity in DR5::GUS-transformed seedlings compared to the control, but induction by auxin and gibberellin in combination is synergistic. Cytokinin increases auxin transport in Arabidopsis seedlings. Auxin, gibberellin, and cytokinin all increase GUS activity in shoots of PsPK2::GUS transformed plants compared to the control. However, only auxin and gibberellin increase GUS activity in PID::GUS shoots. In conclusion, auxin, gibberellin, and cytokinin positively regulate PsPK2 expression in shoots, but not in roots. Auxin and gibberellin also upregulate AtPIN1 and LEAFY expression, which is similar to PsPIN1 and Uni in pea. With minor exceptions, the orthologous genes from both species are regulated similarly.     

Catalysis and regulation: Proteins: Web alert

A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology.     

Focus: Microbiome: Gut Microbiome and Infant Health: Brain-Gut-Microbiota Axis and Host Genetic Factors

The development of the neonatal gut microbiome is influenced by multiple factors, such as delivery mode, feeding, medication use, hospital environment, early life stress, and genetics. The dysbiosis of gut microbiota persists during infancy, especially in high-risk preterm infants who experience lengthy stays in the Neonatal intensive care unit (NICU). Infant microbiome evolutionary trajectory is essentially parallel with the host (infant) neurodevelopmental process and growth. The role of the gut microbiome, the brain-gut signaling system, and its interaction with the host genetics have been shown to be related to both short and long term infant health and bio-behavioral development. The investigation of potential dysbiosis patterns in early childhood is still lacking and few studies have addressed this host-microbiome co-developmental process. Further research spanning a variety of fields of study is needed to focus on the mechanisms of brain-gut-microbiota signaling system and the dynamic host-microbial interaction in the regulation of health, stress and development in human newborns.     

Afterword: Primitivist Encounters: Articulations and Asymmetries

ABSTRACT

This afterword presents a view of key contributions of the issue's articles, positions those contributions in relation to precedent work, and suggests the need to place heightened emphasis on fundamental asymmetry and differential power to determine context on the part of participants to primitivist tourist encounter.     

Focus: Microbiome: Metagenomic Assembly: Overview,Challenges and Applications

Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems.     

Cement Manufacture and the Environment: Part I: Chemistry and Technology

Hydraulic (chiefly portland) cement is the binding agent in concrete and mortar and thus a key component of a country's construction sector. Concrete is arguably the most abundant of all manufactured solid materials. Portland cement is made primarily from finely ground clinker, which itself is composed dominantly of hydraulically active calcium silicate minerals formed through high-temperature burning of limestone and other materials in a kiln. This process requires approximately 1.7 tons of raw materials per ton of clinker produced and yields about 1 ton of carbon dioxide (CO2) emissions, of which cal-cination of limestone and the combustion of fuels each con-tribute about half. The overall level of CO2 output makes the cement industry one of the top two manufacturing industry sources of greenhouse gases; however, in many countries, the cement industry's contribution is a small fraction of that from fossil fuel combustion by power plants and motor vehicles. The nature of clinker and the enormous heat requirements of its manufacture allow the cement industry to consume a wide variety of waste raw materials and fuels, thus providing the opportunity to apply key concepts of industrial ecology, most notably the closing of loops through the use of by-products of other industries (industrial symbiosis).
In this article, the chemistry and technology of cement manufacture are summarized. In a forthcoming companion ar-ticle (part II), some of the environmental challenges and op-portunities facing the cement industry are described. Because of the size and scope of the U.S. cement industry, the analysis relies primarily on data and practices from the United States.