Establishing and maintaining beneficial interactions between the host and its associated microbiota are key requirements for host health. Although the gut microbiota has previously been studied in the context of inflammatory diseases, it has recently become clear that this microbial community has a beneficial role during normal homeostasis, modulating the host's immune system as well as influencing host development and physiology, including organ development and morphogenesis, and host metabolism. The underlying molecular mechanisms of host-microorganism interactions remain largely unknown, but recent studies have begun to identify the key signalling pathways of the cross-species homeostatic regulation between the gut microbiota and its host.

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The gut microbiota — masters of host development and physiology

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

/pdf/animals-in-a-bacterial-world-a-new-imperative-for-the-life-114xzos8tm.pdf

Animals in a bacterial world, a new imperative for the life sciences

As companies strive to develop artefacts intended for services instead of traditional sell-off, new challenges in the product development process arise to promote continuous improvement and increasing market profits. This creates a focus on product life-cycle components as companies then make life-cycle commitments, where they are responsible for the function availability during the extent of the life-cycle, i.e. functional products. One of these life-cycle components is manufacturing; therefore, companies search for new approaches of success during manufacturability evaluation already in engineering design. Efforts have been done to support early engineering design, as this phase sets constraints and opportunities for manufacturing. These efforts have turned into design for manufacturing methods and guidelines. A further step to improve the life-cycle focus during early engineering design is to reuse results and use experience from earlier projects. However, because results and experiences created during project work are often not documented for reuse, only remembered by some people, there is a need for design support. Knowledge engineering (KE) is a methodology for creating knowledge-based systems, e.g. systems that enable reuse of earlier results and make available both explicit and tacit corporate knowledge, enabling the automated generation and evaluation of new engineering design solutions during early product development. There are a variety of KE-approaches, such as knowledge-based engineering, case-based reasoning and programming, which have been used in research to develop design for manufacturing methods and applications. There are, however, opportunities for research where several approaches and their interdependencies, to create a transparent picture of how KE can be used to support engineering design, are investigated. The aim of the research presented in this thesis is to create new methods for design for manufacturing, by using several approaches of KE, and find the beneficial and less beneficial aspects of these methods in comparison to each other and earlier research. This thesis presents methods and applications for design for manufacturing using KE. KE has been employed in several ways, namely rule-based, rule-, programmingand finite element analysis (FEA)-based, and ruleand plan-based, which are tested and compared with each other. Results show that KE can be used to generate information about manufacturing in several ways. The rule-based way is suitable for supporting life-cycle commitments, as engineering design and manufacturing can be integrated with maintenance and performance predictions during early engineering design, though limited to the firing of production rules. The rule-, programmingand FEA-based way can be used to integrate computer-aided design tools and virtual manufacturing for non-linear stress and displacement analysis. This way may also bridge the gap between engineering designers and computational experts, even though this way requires a larger effort to program than the rule-based. The ruleand planbased way can enable design for manufacturing in two fashions – based on earlier manufacturing plans and based on rules. Because earlier manufacturing plans, together with programming algorithms, can handle knowledge that may be more intricate to capture as rules, as opposed to the time demanding routine work that is often automated by means of rules, several opportunities for designing for manufacturing exist.

Methods and Applications

Nitrogen is generally considered one of the major limiting nutrients in plant growth. The biological process responsible for reduction of molecular nitrogen into ammonia is referred to as nitrogen fixation. A wide diversity of nitrogen-fixing bacterial species belonging to most phyla of the Bacteria domain have the capacity to colonize the rhizosphere and to interact with plants. Leguminous and actinorhizal plants can obtain their nitrogen by association with rhizobia or Frankia via differentiation on their respective host plants of a specialized organ, the root nodule. Other symbiotic associations involve heterocystous cyanobacteria, while increasing numbers of nitrogen-fixing species have been identified as colonizing the root surface and, in some cases, the root interior of a variety of cereal crops and pasture grasses. Basic and advanced aspects of these associations are covered in this review.

/pdf/nitrogen-fixing-bacteria-associated-with-leguminous-and-non-1gzxmeeigu.pdf

Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants

Secondary thickening in pteridophytes.-The known cases of secondary thickening in recent Pteridophyta have been brought together by HILL23 in a useful resume. After stating the criteria for secondary growth, Botrychium, which has a distinct cambium, and Ophioglossum, which lacks a definite layer, are described, followed by Angiopteris and Marattia, in which a cambium forms a few xylem elements. CORMACK'S observations on the secondary wood in the nodes of Equisetum are cited, though no reference is made to the cambium in the young cone as reported by J]FFREY.24 The other cases of secondary growth include Psilotum, Selaginella spinulosa, and several species of Isoetes, especially I. hystrix, which may show a cambium outside the vascular cylinder.-M. A.

The Cell Wall

Incidences of coral disease in the Indo-Pacific are increasing at an alarming rate In particular, Montipora white syndrome, a tissue-loss disease found on corals throughout the Hawaiian archipelago, has the potential to degrade Hawaii’s reefs To identify the etiologic agent of Montipora white syndrome, bacteria were isolated from a diseased fragment of Montipora capitata and used in a screen for virulent strains A single isolate, designated strain OCN002, recreated disease signs in 53% of coral fragments in laboratory infection trials when added to a final concentration of 107 cells/ml of seawater In addition to displaying similar signs of disease, diseased coral fragments from the field and those from infection trials both had a dramatic increase in the abundance of associated culturable bacteria, with those of the genus Vibiro well represented Bacteria isolated from diseased fragments used in infection trails were shown to be descendants of the original OCN002 inocula based on both the presence of a plasmid introduced to genetically tag the strain and the sequence of a region of the OCN002 genome In contrast, OCN002 was not re-isolated from fragments that were exposed to the strain but did not develop tissue loss Sequencing of the rrsH gene, metabolic characterization, as well as multilocus sequence analysis indicated that OCN002 is a strain of the recently described species Vibrio owensii This investigation of Montipora white syndrome recognizes V owensii OCN002 as the first bacterial coral pathogen identified from Hawaii’s reefs and expands the range of bacteria known to cause disease in corals

/pdf/vibrio-owensii-induces-the-tissue-loss-disease-montipora-k5s38adm32.pdf

Vibrio owensii Induces the Tissue Loss Disease Montipora White Syndrome in the Hawaiian Reef Coral Montipora capitata

Identification of a pathogen is a critical first step in the epidemiology and subsequent management of a disease. A limited number of pathogens have been identified for diseases contributing to the global decline of coral populations. Here we describe Vibrio coralliilyticus strain OCN008, which induces acute Montipora white syndrome (aMWS), a tissue loss disease responsible for substantial mortality of the coral Montipora capitata in Kāne'ohe Bay, Hawai'i. OCN008 was grown in pure culture, recreated signs of disease in experimentally infected corals, and could be recovered after infection. In addition, strains similar to OCN008 were isolated from diseased coral from the field but not from healthy M. capitata. OCN008 repeatedly induced the loss of healthy M. capitata tissue from fragments under laboratory conditions with a minimum infectious dose of between 10(7) and 10(8) CFU/ml of water. In contrast, Porites compressa was not infected by OCN008, indicating the host specificity of the pathogen. A decrease in water temperature from 27 to 23°C affected the time to disease onset, but the risk of infection was not significantly reduced. Temperature-dependent bleaching, which has been observed with the V. coralliilyticus type strain BAA-450, was not observed during infection with OCN008. A comparison of the OCN008 genome to the genomes of pathogenic V. coralliilyticus strains BAA-450 and P1 revealed similar virulence-associated genes and quorum-sensing systems. Despite this genetic similarity, infections of M. capitata by OCN008 do not follow the paradigm for V. coralliilyticus infections established by the type strain.

Vibrio coralliilyticus Strain OCN008 Is an Etiological Agent of Acute Montipora White Syndrome

Summary


In the filamentous cyanobacterium Anabaena sp. PCC 7120 patS and hetN suppress the differentiation of vegetative cells into nitrogen-fixing heterocysts to establish and maintain a pattern of single heterocysts separated by approximately 10 undifferentiated vegetative cells. Here we show that the patS- and hetN-dependent suppression pathways are the only major factors that prevent vegetative cells from differentiating into heterocysts when a source of ammonia is not present. The patS and hetN pathways are independent of each other, and inactivation of both patS and hetN leads to differentiation of almost all cells of a filament in the absence of a source of fixed nitrogen, compared with approximately 9% in the wild type. Complete differentiation of filaments also occurs when nitrate is supplied as a source of fixed nitrogen, conditions that do not induce differentiation of wild-type filaments. However, ammonia is still capable of suppressing differentiation. The percentage of cells that differentiate into heterocysts appears to be a function of time when a source of fixed nitrogen is absent or a function of growth phase when nitrate is supplied. Although differentiation proceeds unchecked in the absence of patS and hetN expression, differentiation is asynchronous and non-random.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2958.2005.04678.x

Inactivation of patS and hetN causes lethal levels of heterocyst differentiation in the filamentous cyanobacterium Anabaena sp. PCC 7120.

The formation of a pattern of differentiated cells from a group of seemingly equivalent, undifferentiated cells is a central paradigm of developmental biology. Several species of filamentous cyanobacteria differentiate nitrogen-fixing heterocysts at regular intervals along unbranched filaments to form a periodic pattern of two distinct cell types. This patterning has been used to exemplify application of the activator-inhibitor model to periodic patterns in biology. The activator-inhibitor model proposes that activators and inhibitors of differentiation diffuse from source cells to form concentration gradients that in turn mediate patterning, but direct visualization of concentration gradients of activators and inhibitors has been difficult. Here we show that the periodic pattern of heterocysts produced by cyanobacteria relies on two inhibitors of heterocyst differentiation, PatS and HetN, in a manner consistent with the predictions of the activator-inhibitor model. Concentration gradients of the activator, HetR, were observed adjacent to heterocysts, the natural source of PatS and HetN, as well as adjacent to vegetative cells that were manipulated to overexpress a gene encoding either of the inhibitors. Gradients of HetR relied on posttranslational decay of HetR. Deletion of both patS and hetN genes prevented the formation of gradients of HetR, and a derivative of the inhibitors was shown to promote decay of HetR in a concentration-dependent manner. Our results provide strong support for application of the activator-inhibitor model to heterocyst patterning and, more generally, the formation of periodic patterns in biological systems.

https://www.pnas.org/content/pnas/106/47/19884.full.pdf

Genetic and cytological evidence that heterocyst patterning is regulated by inhibitor gradients that promote activator decay

Summary


Differentiation of nitrogen-fixing cells, called heterocysts, by the cyanobacterium Anabaena sp. strain PCC 7120 requires HetR, which is considered the master regulator of heterocyst differentiation. In this study, ectopic expression of hetP from an inducible promoter was shown to partially bypass the need for hetR in heterocyst differentiation. A hetR-deletion strain with hetP expressed ectopically produced cells morphologically similar to heterocysts that produced exopolysaccharide and glycolipids specific to heterocysts, and nitrogenase activity was present under anaerobic conditions, as indicated by an acetylene reduction assay. Five potential transcription start points or transcript processing sites located at positions −727, −545, −208, −177 and −12 bp relative to the putative translational start site were identified in the promoter region of hetP. Relative levels of transcription and their location in filaments resembled that previously reported for HetR protein in various genetic backgrounds, and an inverted repeat sequence in the promoter of hetP was necessary for binding of HetR. Two of the three identified homologues of hetP found in PCC 7120 partially complemented a hetP-null mutant. Taken together, these results suggest that HetP functions directly downstream of HetR in the regulatory network responsible for heterocyst differentiation.

Sean M. Callahan

Papers

Vibrio owensii Induces the Tissue Loss Disease Montipora White Syndrome in the Hawaiian Reef Coral Montipora capitata

Vibrio coralliilyticus Strain OCN008 Is an Etiological Agent of Acute Montipora White Syndrome

Inactivation of patS and hetN causes lethal levels of heterocyst differentiation in the filamentous cyanobacterium Anabaena sp. PCC 7120.

Genetic and cytological evidence that heterocyst patterning is regulated by inhibitor gradients that promote activator decay

Ectopic expression of hetP can partially bypass the need for hetR in heterocyst differentiation by Anabaena sp. strain PCC 7120.