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Amphioxus

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https://www.readbyqxmd.com/read/27869224/selection-of-reliable-reference-genes-for-normalization-of-quantitative-rt-pcr-from-different-developmental-stages-and-tissues-in-amphioxus
#1
Qi-Lin Zhang, Qian-Hua Zhu, Xin Liao, Xiu-Qiang Wang, Tao Chen, Han-Ting Xu, Juan Wang, Ming-Long Yuan, Jun-Yuan Chen
Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder)...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27765604/functional-characterization-of-vitellogenin_n-domain-domain-of-unknown-function-1943-and-von-willebrand-factor-type-d-domain-in-vitellogenin-of-the-non-bilaterian-coral-euphyllia-ancora-implications-for-emergence-of-immune-activity-of-vitellogenin-in-basal
#2
Xiaoyuan Du, Xia Wang, Su Wang, Yang Zhou, Yu Zhang, Shicui Zhang
Our understanding of the function of vitellogenin (Vg) in reproduction has undergone a transformation over the past decade in parallel with new insights into the role of Vg in immunity. However, the time when Vg was endowed with immunological activities during animal evolution remains elusive. Here we demonstrate for the first time that the recombinant proteins rVitellogenin_N, rDUF1943, and rVWD from Vg of the basal metazoan coral Euphyllia ancora not only interact with Gram-positive and negative bacteria as well as their conserved surface components LTA and LPS but also enhance phagocytosis of bacteria by macrophages...
February 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27734831/soxe-neofunctionalization-and-elaboration-of-the-neural-crest-during-chordate-evolution
#3
Andrew Tai, Martin Cheung, Yong-Heng Huang, Ralf Jauch, Marianne E Bronner, Kathryn S E Cheah
During chordate evolution, two genome-wide duplications facilitated acquisition of vertebrate traits, including emergence of neural crest cells (NCCs), in which neofunctionalization of the duplicated genes are thought to have facilitated development of craniofacial structures and the peripheral nervous system. How these duplicated genes evolve and acquire the ability to specify NC and their derivatives are largely unknown. Vertebrate SoxE paralogues, most notably Sox9/10, are essential for NC induction, delamination and lineage specification...
October 13, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27613144/a-new-ldla-domain-containing-c-type-lectin-with-bacterial-agglutinating-and-binding-activity-in-amphioxus
#4
Baozhen Qu, Shuangshuang Yang, Zengyu Ma, Zhan Gao, Shicui Zhang
Over 1200 C-type lectin gene models have been identified in amphioxus, but only a few of them have been functionally characterized. In this study, we identified a C-type lectin, BjCTL, with domain structure of LDLa-CTLD-EGF_Lam, the first such data in chordates. It was expressed mainly in the notochord and ovary in a tissue-dependent fashion. Recombinant BjCTL was characterized as a typical Ca(2+)-dependent carbohydrate-binding protein capable of agglutinating and binding to both Gram-negative and positive bacteria we tested...
December 15, 2016: Gene
https://www.readbyqxmd.com/read/27502435/functional-constraints-on-soxe-proteins-in-neural-crest-development-the-importance-of-differential-expression-for-evolution-of-protein-activity
#5
Eric M Lee, Tian Yuan, Reyna D Ballim, Kristy Nguyen, Robert N Kelsh, Daniel M Medeiros, David W McCauley
Vertebrate SoxE genes (Sox8, 9, and 10) are key regulators of neural crest cell (NCC) development. These genes arose by duplication from a single SoxE gene in the vertebrate ancestor. Although SoxE paralogs are coexpressed early in NCC development, later, Sox9 is restricted to skeletogenic lineages in the head, and Sox10 to non-skeletogenic NCC in the trunk and head. When this subfunctionalization evolved and its possible role in the evolution of the neural crest are unknown. Sea lampreys are basal vertebrates that also possess three SoxE genes, while only a single SoxE is present in the cephalochordate amphioxus...
October 1, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27476717/putative-extremely-high-rate-of-proteome-innovation-in-lancelets-might-be-explained-by-high-rate-of-gene-prediction-errors
#6
László Bányai, László Patthy
A recent analysis of the genomes of Chinese and Florida lancelets has concluded that the rate of creation of novel protein domain combinations is orders of magnitude greater in lancelets than in other metazoa and it was suggested that continuous activity of transposable elements in lancelets is responsible for this increased rate of protein innovation. Since morphologically Chinese and Florida lancelets are highly conserved, this finding would contradict the observation that high rates of protein innovation are usually associated with major evolutionary innovations...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27412606/conserved-noncoding-elements-in-the-most-distant-genera-of-cephalochordates-the-goldilocks-principle
#7
Jia-Xing Yue, Iryna Kozmikova, Hiroki Ono, Carlos W Nossa, Zbynek Kozmik, Nicholas H Putnam, Jr-Kai Yu, Linda Z Holland
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...
2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27368095/evidence-of-g-o-d-s-miracle-unearthing-a-rag-transposon
#8
COMMENT
Martin F Flajnik
Diversity of antibodies and T cell receptors is generated by gene rearrangement dependent on RAG1 and RAG2, enzymes predicted to have been derived from a transposable element (TE) that invaded an immunoglobulin superfamily gene early in the evolution of jawed vertebrates. Now, Huang et al. report the discovery of ProtoRAG in the lower chordate Amphioxus, the long-anticipated TE related to the RAG transposon.
June 30, 2016: Cell
https://www.readbyqxmd.com/read/27329687/a-zebrafish-intelectin-ortholog-agglutinates-both-gram-negative-and-gram-positive-bacteria-with-binding-capacity-to-bacterial-polysaccharide
#9
Lei Chen, Jie Yan, Weiping Sun, Yan Zhang, Chao Sui, Jing Qi, Yijun Du, Lijun Feng
Intelectins are glycan-binding lectins found in various species including cephalochordates, urochordates, fish, amphibians and mammals. But their detailed functions are not well studied in zebrafish which is a good model to study native immunity. In this study, we cloned a zebrafish intelectin ortholog, zebrafish intelectin 2 (zITLN2), which contains a conserved fibrinogen-related domain (FReD) in the N-terminus and the unique intelectin domain in the C-terminus. We examined the tissue distribution of zITLN2 in adult zebrafish and found that zITLN2 was expressed in various organs with the highest level in intestine...
August 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27318694/tracing-the-evolutionary-origin-of-vertebrate-skeletal-tissues-insights-from-cephalochordate-amphioxus
#10
Luok Wen Yong, Jr-Kai Yu
Vertebrate mineralized skeletal tissues are widely considered as an evolutionary novelty. Despite the importance of these tissues to the adaptation and radiation of vertebrate animals, the evolutionary origin of vertebrate skeletal tissues remains largely unclear. Cephalochordates (Amphioxus) occupy a key phylogenetic position and can serve as a valuable model for studying the evolution of vertebrate skeletal tissues. Here we summarize recent advances in amphioxus developmental biology and comparative genomics that can help to elucidate the evolutionary origins of the vertebrate skeletal tissues and their underlying developmental gene regulatory networks (GRN)...
June 16, 2016: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27311567/the-evolution-of-genes-encoding-for-green-fluorescent-proteins-insights-from-cephalochordates-amphioxus
#11
Jia-Xing Yue, Nicholas D Holland, Linda Z Holland, Dimitri D Deheyn
Green Fluorescent Protein (GFP) was originally found in cnidarians, and later in copepods and cephalochordates (amphioxus) (Branchiostoma spp). Here, we looked for GFP-encoding genes in Asymmetron, an early-diverged cephalochordate lineage, and found two such genes closely related to some of the Branchiostoma GFPs. Dim fluorescence was found throughout the body in adults of Asymmetron lucayanum, and, as in Branchiostoma floridae, was especially intense in the ripe ovaries. Spectra of the fluorescence were similar between Asymmetron and Branchiostoma...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27307516/acquisition-of-the-dorsal-structures-in-chordate-amphioxus
#12
Arseniy R Morov, Tharcisse Ukizintambara, Rushan M Sabirov, Kinya Yasui
Acquisition of dorsal structures, such as notochord and hollow nerve cord, is likely to have had a profound influence upon vertebrate evolution. Dorsal formation in chordate development thus has been intensively studied in vertebrates and ascidians. However, the present understanding does not explain how chordates acquired dorsal structures. Here we show that amphioxus retains a key clue to answer this question. In amphioxus embryos, maternal nodal mRNA distributes asymmetrically in accordance with the remodelling of the cortical cytoskeleton in the fertilized egg, and subsequently lefty is first expressed in a patch of blastomeres across the equator where wnt8 is expressed circularly and which will become the margin of the blastopore...
June 2016: Open Biology
https://www.readbyqxmd.com/read/27268975/what-are-head-cavities-a-history-of-studies-on-vertebrate-head-segmentation
#13
Shigeru Kuratani, Noritaka Adachi
Motivated by the discovery of segmental epithelial coeloms, or "head cavities," in elasmobranch embryos toward the end of the 19th century, the debate over the presence of mesodermal segments in the vertebrate head became a central problem in comparative embryology. The classical segmental view assumed only one type of metamerism in the vertebrate head, in which each metamere was thought to contain one head somite and one pharyngeal arch, innervated by a set of cranial nerves serially homologous to dorsal and ventral roots of spinal nerves...
June 2016: Zoological Science
https://www.readbyqxmd.com/read/27265651/expression-analysis-of-eight-amphioxus-genes-involved-in-the-wnt-%C3%AE-catenin-signaling-pathway
#14
Jing Wang, Guang Li, Guang-Hui Qian, Jun-Hao Hua, Yi-Quan Wang
The Wnt/β-catenin signaling pathway plays a crucial role in the embryonic development of metazoans. Although the pathway has been studied extensively in many model animals, its function in amphioxus, the most primitive chordate, remains largely uncharacterized. To obtain basic data for functional analysis, we identified and isolated seven genes (Lrp5/6, Dvl, APC, CkIα, CkIδ, Gsk3β, and Gro) of the Wnt/β-catenin signaling pathway from the amphioxus (Branchiostoma floridae) genome. Phylogenetic analysis revealed that amphioxus had fewer members of each gene family than that found in vertebrates...
May 18, 2016: Dong Wu Xue Yan Jiu, Zoological Research
https://www.readbyqxmd.com/read/27216767/allohahella-marinimesophila-gen-nov-sp-nov-isolated-from-seawater-and-reclassification-of-hahella-antarctica-as-allohahella-antarctica-comb-nov
#15
Yanqiong Han, Rui Zhao, Tong Yu, Zhao Li, Xiao-Hua Zhang
A Gram-stain-negative, non-endospore-forming, strictly aerobic, irregular rod-shaped bacterium without flagellum, designated strain H94T, was isolated by the high-throughput cultivation method from seawater of an amphioxus breeding zone in the coastal region of Qingdao, China. Growth was observed at 4-37 °C (optimum 28 °C), at pH 6.0-10.0 (optimum pH 7.0) and in the presence of 1-12 % (w/v) NaCl (optimum 1-2 %). The predominant cellular fatty acids were C18 : 1ω9c, C16 : 0 and C16 : 1ω9c...
September 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27166696/zoology-a-new-mouth-for-amphioxus
#16
Vladimir Soukup, Zbynek Kozmik
Deuterostomes - a key subdivision of animals - are characterized by the mouth developing anteriorly as a rupture between the outer epithelium and the foregut wall. A new study of amphioxus challenges this view and proposes separate evolutionary origins of deuterostome oral openings.
May 9, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27069919/neurotrophin-p75-and-trk-signaling-module-in-the-developing-nervous-system-of-the-marine-annelid-platynereis-dumerilii
#17
Antonella Lauri, Paola Bertucci, Detlev Arendt
In vertebrates, neurotrophic signaling plays an important role in neuronal development, neural circuit formation, and neuronal plasticity, but its evolutionary origin remains obscure. We found and validated nucleotide sequences encoding putative neurotrophic ligands (neurotrophin, NT) and receptors (Trk and p75) in two annelids, Platynereis dumerilii (Errantia) and Capitella teleta (Sedentaria, for which some sequences were found recently by Wilson, 2009). Predicted protein sequences and structures of Platynereis neurotrophic molecules reveal a high degree of conservation with the vertebrate counterparts; some amino acids signatures present in the annelid Trk sequences are absent in the basal chordate amphioxus, reflecting secondary loss in the cephalochordate lineage...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27054569/normal-development-and-experimental-embryology-edmund-beecher-wilson-and-amphioxus
#18
James W E Lowe
This paper concerns the concept of normal development, and how it is enacted in experimental procedures. To that end, I use an historical case study to assess the three ways in which normal development is and has been produced, used, and interpreted in the practice of experimental biology. I argue that each of these approaches involves different processes of abstraction, which manage biological variation differently. I then document the way in which Edmund Beecher Wilson, a key contributor to late-nineteenth century experimental embryology, approached the study of normal development and show that his work does not fit any of the three established categories in the taxonomy...
June 2016: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/26979494/transcriptome-analysis-of-different-developmental-stages-of-amphioxus-reveals-dynamic-changes-of-distinct-classes-of-genes-during-development
#19
Kevin Yi Yang, Yuan Chen, Zuming Zhang, Patrick Kwok-Shing Ng, Wayne Junwei Zhou, Yinfeng Zhang, Minghua Liu, Junyuan Chen, Bingyu Mao, Stephen Kwok-Wing Tsui
Vertebrates diverged from other chordates approximately 500 million years ago and have adopted several modifications of developmental processes. Amphioxus is widely used in evolutionary developmental biology research, such as on the basic patterning mechanisms involved in the chordate body plan and the origin of vertebrates. The fast development of next-generation sequencing has advanced knowledge of the genomic organization of amphioxus; however, many aspects of gene regulation during amphioxus development have not been fully characterized...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26940763/tcf-lef-regulates-the-gsx-parahox-gene-in-central-nervous-system-development-in-chordates
#20
Myles G Garstang, Peter W Osborne, David E K Ferrier
BACKGROUND: The ParaHox genes play an integral role in the anterior-posterior (A-P) patterning of the nervous system and gut of most animals. The ParaHox cluster is an ideal system in which to study the evolution and regulation of developmental genes and gene clusters, as it displays similar regulatory phenomena to its sister cluster, the Hox cluster, but offers a much simpler system with only three genes. RESULTS: Using Ciona intestinalis transgenics, we isolated a regulatory element upstream of Branchiostoma floridae Gsx that drives expression within the central nervous system of Ciona embryos...
2016: BMC Evolutionary Biology
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