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The Marine Biological Reference Collections (CBMR) are located at the Institute of Marine Sciences (ICM-CSIC) in Barcelona, Spain. The CBR are a Unit of Service where around 15000 referenced species are preserved, catalogued and maintained for their study. The most represented marine groups at the CBMR are fish, crustaceans, molluscs and echinoderms, but also other groups are present. The studies based on the CBMR specimens are focused on biodiversity, biogeography, taxonomy (type species), invasive and alien species, and genetic analysis. Several PhD theses have also been carried out in collaboration with the CBMR.The CBMR are a reference point for the marine biodiversity of the Mediterranean Sea, but in their facilities the CBMR also hold specimens from all the oceans (Atlantic, Pacific, Indian, Antarctic and Arctic). The Collections are constantly receiving new specimens and updating. The main sources of specimens are oceanographic surveys and different kind of sampling programs carried out by the research projects run by the ICM-CSIC. However, the CBMR have also received (in the past and currently) different collections donated by naturalists, researchers, other institutions, and particulars. The CBMR were created in 1981, in the earlier history of the ICM-CSIC, by Jaume Rucabado, Domingo Lloris and Concepción Allué. The Collections were later recognized and catalogued by the Spanish Ministry of Culture in 1990. In the last decade, the CBMR initiated a new stage where the information was digitized and the physical preservation of specimens updated to the new rules (such as change from formaldehyde to ethanol). The CBMR are now part of GBIF (Global Biodiversity Information Facility), thus making public and available all data collections and their metadata. We have also incorporated the use of Geographical Information Systems (GIS) to monitor and study the geographical distribution of our specimens and moreover, the CBMR started to act as repository of DNA voucher

Understanding how neurons regenerate following injury remains a central challenge in regenerative medicine. Adult mammals have a very limited ability to regenerate new neurons in the central nervous system (CNS). In contrast, the basal chordate Polycarpa mytiligera can regenerate its entire CNS within seven days of complete removal. Transcriptome sequencing, cellular labeling, and proliferation in vivo essays revealed that CNS regeneration is mediated by a newly formed neural progeny and the activation of neurodevelopmental pathways that are associated with enhanced stem-cell activity. Analyzing the expression of 239 activated pathways enabled a quantitative understanding of gene-set enrichment patterns at key regeneration stages. The molecular and cellular mechanisms controlling the regenerative ability that this study reveals can be used to develop innovative approaches to enhancing neurogenesis in closely-related chordate species, including humans.

In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth's eukaryotic diversity [H. A. Lewin et al., Proc. Natl. Acad. Sci. U.S.A. 115, 4325-4333 (2018)]. As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline's future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies in GenBank, the world's most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for improving genomic resource availability and research value while also broadening global representation.

The fluvial, overbank, and lacustrine deposits of the Upper Jurassic Morrison Formation of the Western Interior, U.S.A. have been intensively studied due to their diverse and well-preserved dinosaurian fauna, and the presence of economic quantities of uranium and vanadium ores. The formation crops out over 12 degrees of latitude and 1.2 million km2, and is an excellent case study for the examination of paleoecology, community structure, and evolutionary dynamics at a time in Earth's history when the climate was significantly warmer than today. However, paleoecological studies have been hampered by lack of correlation across the formation. Assuming a primarily tectonic control on fluvial architecture, we propose the first chronostratigraphic framework of the formation, which is based on sequence stratigraphy, magnetostratigraphy, and radiometric dating. The formation can be divided into three sequences each represented by a period of degradation followed by aggradation. This chronostratigraphic framework indicates that the formation youngs to the north, and was deposited over about 7 million years during the late Kimmeridgian and Tithonian. This framework provides a foundation for future sedimentological, stratigraphic, and paleobiological studies of the iconic dinosaurian fauna known from the Morrison., The attached document is the authors’ final accepted/submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it., NHM Repository

Two species of styelid colonial ascidians in the genus Syncarpa Redikorzev, 1913 are known from the northwest Pacific. The valid status of the lesser known species, Syncarpa composita (Tokioka, 1951) (type locality: Akkeshi, Japan), is assessed here. To assess the taxonomic identity of S. composita, we compared one of the syntypes and freshly collected topotypes of S. composita with a syntype of S. oviformis Redikorzev, 1913 (type locality: Mandril Bay, Russia). Specimens of S. composita consistently differed from the syntype of S. ovifermis in the number of oral tentacles, the number of size-classes of transverse vessels, and the number of anal lobes. In this paper, S. composita is redescribed as distinct from S. oviformis, and its phylogenetic position inferred within Styelidae based on the 18S rRNA and cytochrome c oxidase subunit I gene sequences. In our phylogenetic tree, Syncarpa formed a well-supported Bade together with Dendrodoa MacLeay, 1824. In Syncarpa and Dendrodoa, a single gonad is situated on the right side of the body, which is unique among Styelidae, and thus can be a synapomorphy for this clade.

Two species of styelid colonial ascidians in the genus Syncarpa Redikorzev, 1913 are known from the northwest Pacific. The valid status of the lesser known species, Syncarpa composita (Tokioka, 1951) (type locality: Akkeshi, Japan), is assessed here. To assess the taxonomic identity of S. composita, we compared one of the syntypes and freshly collected topotypes of S. composita with a syntype of S. oviformis Redikorzev, 1913 (type locality: Mandril Bay, Russia). Specimens of S. composita consistently differed from the syntype of S. ovifermis in the number of oral tentacles, the number of size-classes of transverse vessels, and the number of anal lobes. In this paper, S. composita is redescribed as distinct from S. oviformis, and its phylogenetic position inferred within Styelidae based on the 18S rRNA and cytochrome c oxidase subunit I gene sequences. In our phylogenetic tree, Syncarpa formed a well-supported Bade together with Dendrodoa MacLeay, 1824. In Syncarpa and Dendrodoa, a single gonad is situated on the right side of the body, which is unique among Styelidae, and thus can be a synapomorphy for this clade.

In order to interpret fossil and sub-fossil associations of vertebrates, it is important to understand how carcasses degrade in nature. Here we describe the process of bone loss from of 32 carcasses from eight species of terrestrial mammals over two to 63 months in two Mediterranean ecosystems in the southwest of the Iberian Peninsula. The carcasses ranged in mass from 5 kg to over 450 kg. These data allow the quantitative description of the dynamics of degradation in three time phases defined by changes in the rate of bone loss as measured by the Skeletal Conservation Index (SCI). The SCI values estimated for each phase of degradation is considered the fossil potentiality of the carcass. In the first phase, very few bones were lost, followed by a phase of high bone loss driven by scavengers. The rate of bone loss reduced greatly again in the final phase, which was driven primarily by abiotic, environmental factors. The largest carcasses spend a longer time in each phase, and also had a higher SCI at the end of Phase II. The smallest carcasses experienced a much higher variance in degradation, had significantly lower SCI, and many of the smallest carcasses were consumed completely in a short period of time. Differences between localities were observed regarding SCI values. Presence or absence of tree coverage in the place where the carcass was located also had a significant effect on SCI. These data highlight the importance of considering the contemporaneous scavengers when interpreting animals from paleontological contexts. These data also explain the bias observed in many ancient sites whereby larger animals are over represented.

Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.

We studied the ascidian fauna from two zones located in subantarctic (Punta Arenas, latitude 53º) and temperate Chile (Coquimbo, latitude 29º). The different oceanographic features of the two zones, with influence of the Humboldt Current in the north and the Cape Horn Current System and freshwater inputs in the south, led to markedly different ascidian faunas. A total of 22 species were recorded, with no shared species across the two areas (11 species each). The new species Polyzoa iosune is described, Lissoclinum perforatum is found for the first time in the Pacific Ocean, and Synoicum georgianum and Polyzoa minor are new to the Chilean fauna. The populations of Ciona in the Coquimbo area (formerly attributed to Ciona intestinalis) correspond to the species Ciona robusta. A total of 35 Cytochrome oxidase (COI) sequences of the standard barcode region have been obtained for 17 of the 22 species reported.

In the past 40 years, comparisons of developmental gene expression and mechanisms of development (evodevo) joined comparative morphology as tools for reconstructing long-extinct ancestral forms. Unfortunately, both approaches typically give congruent answers only with closely related organisms. Chordate nervous systems are good examples. Classical studies alone left open whether the vertebrate brain was a new structure or evolved from the anterior end of an ancestral nerve cord like that of modern amphioxus. Evodevo plus electron microscopy showed that the amphioxus brain has a diencephalic forebrain, small midbrain, hindbrain and spinal cord with parts of the genetic mechanisms for the midbrain/hindbrain boundary, zona limitans intrathalamica and neural crest. Evodevo also showed how extra genes resulting from whole-genome duplications in vertebrates facilitated evolution of new structures like neural crest. Understanding how the chordate central nervous system (CNS) evolved from that of the ancestral deuterostome has been truly challenging. The majority view is that this ancestor had a CNS with a brain that gave rise to the chordate CNS and, with loss of a discrete brain, to one of the two hemichordate nerve cords. The minority view is that this ancestor had no nerve cord; those in chordates and hemichordates evolved independently. New techniques such as phylostratigraphy may help resolve this conundrum.

Acorn worms, also known as enteropneust (literally, gut-breathing) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal gill slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Provi

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Provi

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Es dóna noticia i es descriu una urpa de vertebrat apareguda en una pista del terme municipal d'Argelita (l'Alt Millars), dins la subconca sedimentària del Penyagolosa., A claw of a vertebrate fossil mentioned and described in Argelita (l?Alt Millars, Spain) from Penyagolosa subbasin.

[EN] This article documents the addition of 111 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser oxyrinchus desotoi, Anopheles nuneztovari sensu lato, Asellus aquaticus, Calopteryx splendens, Calopteryx virgo, Centaurea aspera, Centaurea seridis, Chilina dombeyana, Proctoeces cf. lintoni and Pyrenophora teres f. teres. © 2011 Blackwell Publishing Ltd.

[EN] This article documents the addition of 111 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser oxyrinchus desotoi, Anopheles nuneztovari sensu lato, Asellus aquaticus, Calopteryx splendens, Calopteryx virgo, Centaurea aspera, Centaurea seridis, Chilina dombeyana, Proctoeces cf. lintoni and Pyrenophora teres f. teres. © 2011 Blackwell Publishing Ltd.

We examined the prevalence of antibodies to zoonotic protozoan parasites (Trypanosoma cruzi, Toxoplasma gondii, and Encephalitozoon cuniculi) and protozoans of veterinary importance (Neospora caninum, Sarcocystis neurona, and Besnoitia darlingi) in a population of North American opossums (Didelphis virginiana) from Louisiana. Samples from 30 opossums were collected as part of a survey for T. cruzi in Louisiana. Frozen sera from these 30 opossums were examined using an indirect immunofluorescent antibody test (IFAT) against in vitro-produced antigenic stages of these protozoans. Additionally, 24 of the 30 samples were examined using hemoculture, and all 30 were examined in the modified direct agglutination test (MAT) for antibodies to To. gondii. The prevalences of reactive IFAT samples were as follows: 60% for T. cruzi, 27% for To. gondii, 23% for E. cuniculi, 17% for S. neurona, 47% for B. darlingi, and 0% for N. caninum. Hemoculture revealed that 16 (67%) of 24 samples were positive for T. cruzi, compared to 18 of 30 (60%) by IFAT. The sensitivity and specificity for the IFAT compared to hemoculture was 100% for each. The modified direct agglutination test revealed that 9 (30%) of the 30 samples from opossums had antibodies to To. gondii, compared to 8 (27%) using the IFAT. The sensitivity and specificity of the IFAT compared to the MAT was 100% and 72%, respectively.

We examined the prevalence of antibodies to zoonotic protozoan parasites (Trypanosoma cruzi, Toxoplasma gondii, and Encephalitozoon cuniculi) and protozoans of veterinary importance (Neospora caninum, Sarcocystis neurona, and Besnoitia darlingi) in a population of North American opossums (Didelphis virginiana) from Louisiana. Samples from 30 opossums were collected as part of a survey for T. cruzi in Louisiana. Frozen sera from these 30 opossums were examined using an indirect immunofluorescent antibody test (IFAT) against in vitro-produced antigenic stages of these protozoans. Additionally, 24 of the 30 samples were examined using hemoculture, and all 30 were examined in the modified direct agglutination test (MAT) for antibodies to To. gondii. The prevalences of reactive IFAT samples were as follows: 60% for T. cruzi, 27% for To. gondii, 23% for E. cuniculi, 17% for S. neurona, 47% for B. darlingi, and 0% for N. caninum. Hemoculture revealed that 16 (67%) of 24 samples were positive for T. cruzi, compared to 18 of 30 (60%) by IFAT. The sensitivity and specificity for the IFAT compared to hemoculture was 100% for each. The modified direct agglutination test revealed that 9 (30%) of the 30 samples from opossums had antibodies to To. gondii, compared to 8 (27%) using the IFAT. The sensitivity and specificity of the IFAT compared to the MAT was 100% and 72%, respectively.

BackgroundRegulation in protein networks often utilizes specialized domains that 'join' (or 'connect') the network through specific protein-protein interactions. The innate immune system, which provides a first and, in many species, the only line of defense against microbial and viral pathogens, is regulated in this way. Amphioxus (Branchiostoma floridae), whose genome was recently sequenced, occupies a unique position in the evolution of innate immunity, having diverged within the chordate lineage prior to the emergence of the adaptive immune system in vertebrates.ResultsThe repertoire of several families of innate immunity proteins is expanded in amphioxus compared to both vertebrates and protostome invertebrates. Part of this expansion consists of genes encoding proteins with unusual domain architectures, which often contain both upstream receptor and downstream activator domains, suggesting a potential role for direct connections (shortcuts) that bypass usual signal transduction pathways.ConclusionDomain rearrangements can potentially alter the topology of protein-protein interaction (and regulatory) networks. The extent of such arrangements in the innate immune network of amphioxus suggests that domain shuffling, which is an important mechanism in the evolution of multidomain proteins, has also shaped the development of immune systems.

Ling, Ka Ho., Thesis (M.Phil.)--Chinese University of Hong Kong, 2008., Includes bibliographical references (leaves 124-157)., s in English and Chinese., Acknowledgement --- p.ii, p.iv, 摘要 --- p.vii, Table of content --- p.ix, List of figures --- p.xiii, List of tables --- p.xv, Abbreviations --- p.xvi, Chapter 1 --- Food authentication --- p.1, Chapter 1.1 --- Introduction and definition --- p.1, Chapter 1.2 --- Importance of species identification in food authentication --- p.3, Chapter 1.3 --- Methods for species identification in food authentication --- p.8, Chapter 1.4 --- Legislation --- p.17, Chapter 1.5 --- Objectives --- p.19, Chapter 2 --- Molecular authentication and antitussive bioassay of Stemona root (Baibu) and root of Asparagus filicinus (Xiao-baibu) --- p.20, Chapter 2.1 --- Introduction --- p.20, Chapter 2.2 --- Materials and methods --- p.22, Chapter 2.3 --- Results --- p.34, Chapter 2.4 --- Discussion --- p.40, Chapter 2.5 --- Conclusions --- p.44, Chapter 3 --- Rapid detection of oilfish and escolar in fish steaks: a tool to prevent keriorrhea episodes --- p.45, Chapter 3.1 --- Introduction --- p.45, Chapter 3.2 --- Materials and methods --- p.49, Chapter 3.3 --- Results --- p.59, Chapter 3.4 --- Discussion --- p.69, Chapter 3.5 --- Conclusions --- p.75, Chapter 4 --- Widespread adulteration of crocodile meat with python and water monitor meats --- p.76, Chapter 4.1 --- Introduction --- p.76, Chapter 4.2 --- Materials and methods --- p.78, Chapter 4.3 --- Results --- p.89, Chapter 4.4 --- Discussion --- p.96, Chapter 4.5 --- Conclusions --- p.100, Chapter 5 --- Authentication of dried and ready-to-eat hashima products --- p.101, Chapter 5.1 --- Introduction --- p.101, Chapter 5.2 --- Source species of hashima --- p.103, Chapter 5.3 --- Materials and methods --- p.106, Chapter 5.4 --- Results --- p.116, Chapter 5.5 --- Discussion --- p.119, Chapter 5.6 --- Conclusions --- p.121, Chapter 6 --- General conclusions --- p.122, Chapter 6.1 --- Key findings --- p.122, Chapter 6.2 --- Applications and implications --- p.123, Chapter 7 --- References --- p.124, http://library.cuhk.edu.hk/record=b5893608, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

BackgroundRegulation in protein networks often utilizes specialized domains that 'join' (or 'connect') the network through specific protein-protein interactions. The innate immune system, which provides a first and, in many species, the only line of defense against microbial and viral pathogens, is regulated in this way. Amphioxus (Branchiostoma floridae), whose genome was recently sequenced, occupies a unique position in the evolution of innate immunity, having diverged within the chordate lineage prior to the emergence of the adaptive immune system in vertebrates.ResultsThe repertoire of several families of innate immunity proteins is expanded in amphioxus compared to both vertebrates and protostome invertebrates. Part of this expansion consists of genes encoding proteins with unusual domain architectures, which often contain both upstream receptor and downstream activator domains, suggesting a potential role for direct connections (shortcuts) that bypass usual signal transduction pathways.ConclusionDomain rearrangements can potentially alter the topology of protein-protein interaction (and regulatory) networks. The extent of such arrangements in the innate immune network of amphioxus suggests that domain shuffling, which is an important mechanism in the evolution of multidomain proteins, has also shaped the development of immune systems.

Gastrointestinal disturbances can cause large economic losses in the pig industry. Diseases and conditions of the gastrointestinal tract (GIT) that can cause economic loss have generally been controlled by the use of dietary (and or in the water) antimicrobial compounds, such as antibiotic feed additives and (or) minerals such as zinc and copper. However the implementation of legislation in some parts of the world, for example the European Union, and a growing sentiment worldwide to reduce the use of dietary antimicrobial compounds, has caused a reassessment of measures to influence GIT 'health' and caused enormous interest in alternative means to control diseases and conditions of the GIT. There are now available a wide array of products and strategies available to the pig industry that influence 'gut health'. The products in the market place are characterised predominately not only by their (claimed) different modes of action, but also by the variation in responses seen when offered to pigs, and not only in the post-weaning period. This variation is presumably a consequence of the many different conditions of management that pigs are under, that in turn influences factors such as composition of the microbiota and mucosal immunity. Other strategies, such as the manipulation of particle size and changing the protein content of a diet, might also be adopted to influence the expression of enteric pathogens and the expression of disease. Ultimately, the cost-benefit of adopting such practices to influence gastrointestinal 'health' requires consideration.

Gastrointestinal disturbances can cause large economic losses in the pig industry. Diseases and conditions of the gastrointestinal tract (GIT) that can cause economic loss have generally been controlled by the use of dietary (and or in the water) antimicrobial compounds, such as antibiotic feed additives and (or) minerals such as zinc and copper. However the implementation of legislation in some parts of the world, for example the European Union, and a growing sentiment worldwide to reduce the use of dietary antimicrobial compounds, has caused a reassessment of measures to influence GIT 'health' and caused enormous interest in alternative means to control diseases and conditions of the GIT. There are now available a wide array of products and strategies available to the pig industry that influence 'gut health'. The products in the market place are characterised predominately not only by their (claimed) different modes of action, but also by the variation in responses seen when offered to pigs, and not only in the post-weaning period. This variation is presumably a consequence of the many different conditions of management that pigs are under, that in turn influences factors such as composition of the microbiota and mucosal immunity. Other strategies, such as the manipulation of particle size and changing the protein content of a diet, might also be adopted to influence the expression of enteric pathogens and the expression of disease. Ultimately, the cost-benefit of adopting such practices to influence gastrointestinal 'health' requires consideration.

Gastrointestinal disturbances can cause large economic losses in the pig industry. Diseases and conditions of the gastrointestinal tract (GIT) that can cause economic loss have generally been controlled by the use of dietary (and or in the water) antimicrobial compounds, such as antibiotic feed additives and (or) minerals such as zinc and copper. However the implementation of legislation in some parts of the world, for example the European Union, and a growing sentiment worldwide to reduce the use of dietary antimicrobial compounds, has caused a reassessment of measures to influence GIT 'health' and caused enormous interest in alternative means to control diseases and conditions of the GIT. There are now available a wide array of products and strategies available to the pig industry that influence 'gut health'. The products in the market place are characterised predominately not only by their (claimed) different modes of action, but also by the variation in responses seen when offered to pigs, and not only in the post-weaning period. This variation is presumably a consequence of the many different conditions of management that pigs are under, that in turn influences factors such as composition of the microbiota and mucosal immunity. Other strategies, such as the manipulation of particle size and changing the protein content of a diet, might also be adopted to influence the expression of enteric pathogens and the expression of disease. Ultimately, the cost-benefit of adopting such practices to influence gastrointestinal 'health' requires consideration.