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Marine Genomics

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https://www.readbyqxmd.com/read/29426805/boveri-s-research-at-the-zoological-station-naples-rediscovery-of-his-original-microscope-slides-at-the-university-of-w%C3%A3-rzburg
#1
Ulrich Scheer
Eric Davidson once wrote about Theodor Boveri: "From his own researches, and perhaps most important, his generalized interpretations, derive the paradigms that underlie modern inquiries into the genomic basis of embryogenesis" (Davidson, 1985). As luck would have it, the "primary data" of Boveri's experimental work, namely the microscope slides prepared by him and his wife Marcella during several stays at the Zoological Station in Naples (1901/02, 1911/12 and 1914), have survived at the University of Würzburg...
February 6, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29395622/prediction-of-a-peptidome-for-the-ecotoxicological-model-hyalella-azteca-crustacea-amphipoda-using-a-de-novo-assembled-transcriptome
#2
Andrew E Christie, Matthew C Cieslak, Vittoria Roncalli, Petra H Lenz, Kaley M Major, Helen C Poynton
Due to its sensitivity to many environmental and anthropogenic stressors, including a wide range of chemical compounds, Hyalella azteca, a freshwater amphipod, has emerged as one of the most commonly used invertebrates for ecotoxicological assessment.Peptidergic signaling systems are key components in the control of organism-environment interactions, and there is a growing literature suggesting that they are targets of a number of aquatic toxicants.Interestingly, and despite its model species status in the field of ecotoxicology, little is known about the peptide hormones of H...
January 30, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29395623/muscle-and-liver-transcriptome-characterization-and-genetic-marker-discovery-in-the-farmed-meagre-argyrosomus-regius
#3
T Manousaki, A Tsakogiannis, J Lagnel, D Kyriakis, N Duncan, A Estevez, C S Tsigenopoulos
Meagre (Argyrosomus regius), a teleost fish of the family Sciaenidae, is part of a group of marine fish species considered new for Mediterranean aquaculture representing the larger fish cultured in the region. Meagre aquaculture started ~25years ago in West Mediterranean, and the supply of juveniles has been dominated by few hatcheries. This fact has raised concerns on possible inbreeding, urging the need for genetic information on the species and for an assessment of the polymorphisms found in the genome. To that end we characterized the muscle and liver transcriptome of a pool of meagre individuals, from different families and phenotypic size, to obtain a backbone that can support future studies regarding physiology, immunology and genetics of the species...
January 21, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29306571/genomic-analyses-of-five-roseivirga-species-insights-into-marine-adaptation
#4
Chitra Selvaratnam, Suganthi Thevarajoo, Kian Mau Goh, Kok-Gan Chan, Chun Shiong Chong
To date, the genus Roseivirga consists of six species with one subspecies and is one of the least-studied genera among the family Flammeovirgaceae. In order to further explore this genus, the genome sequences of five Roseivirga spp. were compared and described in this study. The Roseivirga genomes have similar sizes in the range of 4.08-4.47Mb with an average of 4.22Mb. Several key proteins related to osmotic stress adaptation were identified in Roseivirga spp. including betaine transporter, choline dehydrogenase, and glutamate synthases...
January 3, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29275151/coelacanth-specific-adaptive-genes-give-insights-into-primitive-evolution-for-water-to-land-transition-of-tetrapods
#5
Chul Lee, Heesu Jeong, DongAhn Yoo, Eun Bae Kim, Bo-Hye Nam, Heebal Kim
Coelacanth is a group of extant lobe-finned fishes in Sarcopterygii that provides evolutionary information for the missing link between ray-finned fish and tetrapod vertebrates. Its phenotypes, different from actinopterygian fishes, have been considered as primitive terrestrial traits such as cartilages in their fatty fins which are homologous with the humerus and femur. To investigate molecular evolution of coelacanth which led to its divergence into Sarcopterygii, we compared its protein coding sequences with 11 actinopterygian fishes...
December 20, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29273445/selective-pressure-on-the-protein-coding-genes-of-the-pufferfish-is-correlated-with-phenotypic-traits
#6
Hyeonju Ahn, Chul Lee, Bo-Hye Nam, Eun Bae Kim, Kelsey Caetano-Anolles, Heebal Kim
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database...
December 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29249402/a-phylogenetic-classification-of-gastropod-aquaporins
#7
D J Colgan, R P Santos
Successful responses to the multifarious challenges of controlling water balance are critical for snails' survival in the great diversity of habitats they occupy. Advances are being made in understanding how such challenges are approached at the molecular level, including through the study of aquaporins, which are proteins functioning to facilitate the passage of water and other small molecules across cellular membranes. Deduced aquaporin amino acid sequences from partial genomic assemblies of three neritimorph species were added to available gastropod data and sequences from other taxa to make a phylogenetic classification of these proteins using maximum likelihood and Bayesian analyses...
December 14, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29223543/metagenomic-sequencing-of-environmental-dna-reveals-marine-faunal-assemblages-from-the-west-antarctic-peninsula
#8
Dominique A Cowart, Katherine R Murphy, C-H Christina Cheng
The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods...
December 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29198427/towards-the-identification-of-ancestrally-shared-regenerative-mechanisms-across-the-metazoa-a-transcriptomic-case-study-in-the-demosponge-halisarca-caerulea
#9
Nathan J Kenny, Jasper M de Goeij, Didier M de Bakker, Casey G Whalen, Eugene Berezikov, Ana Riesgo
Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study...
November 29, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29239804/sex-determination-and-differentiation-genes-in-a-functional-hermaphrodite-scallop-nodipecten-subnodosus
#10
Pavel Galindo-Torres, Alejandra García-Gasca, Raúl Llera-Herrera, Cristina Escobedo-Fregoso, Cei Abreu-Goodger, Ana M Ibarra
The lion-paw, Nodipecten subnodosus is one of three scallop species commercially exploited on the west coast of the Peninsula of Baja California. Because nothing is known about sex determination and sexual differentiation in hermaphrodite scallops, in the present work, a global transcriptomic analysis was performed in two early developmental stages, settling eyed-larvae and spat, as well as in three tissues (undifferentiated gonad, digestive gland, and adductor muscle). Over 27 million Illumina paired-end reads were obtained through the MiSeq platform...
November 24, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29175002/complete-genome-sequence-of-granulosicoccus-antarcticus-type-strain-imcc3135t-a-marine-gammaproteobacterium-with-a-putative-dimethylsulfoniopropionate-demethylase-gene
#11
Ilnam Kang, Yeonjung Lim, Jang-Cheon Cho
Granulosicoccus, the only genus of the family Granulosicoccaceae, occupies a distinct phylogenetic position within the order Chromatiales of the Gammaproteobacteria. The genus has been found in various marine regions, especially associated with diverse marine macroalgae. No genomes have been reported for the genus Granulosicoccus thus far, hampering studies on physiology and lifestyles of this genus. Here we report the complete genome sequence of strain IMCC3135T, the type strain of Granulosicoccus antarcticus isolated from Antarctic coastal seawater...
November 23, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29237565/support-marine-biotech
#12
EDITORIAL
Steffen Lüsse
No abstract text is available yet for this article.
December 2017: Marine Genomics
https://www.readbyqxmd.com/read/29237564/application-of-genomics-in-salmon-aquaculture-breeding-programs-by-ashie-norris-who-knows-where-the-genomic-revolution-will-lead-us
#13
Ashie Norris
No abstract text is available yet for this article.
December 2017: Marine Genomics
https://www.readbyqxmd.com/read/29237563/navigating-the-future-cross-sector-marine-genomics
#14
Laura Giuliano, Antje Labes, Marlis Reich, Cinzia Verde
No abstract text is available yet for this article.
December 2017: Marine Genomics
https://www.readbyqxmd.com/read/29074263/novel-subfamilies-of-actin-regulating-proteins
#15
A A Morozov, Ye D Bedoshvili, M S Popova, Ye V Likhoshway
Ability of actin to polymerise and depolymerise makes it essential to key functions of eukaryotic cell. The functioning of actin is controlled by a host of regulatory proteins, the repertoire of which in diatoms is known to remarkably differ from other organisms. We have performed a phylogenetic analysis of 521 actin and actin-related proteins' aminoacid sequences, as well as 190 sequences of gelsolin family proteins from various genomic and transcriptomic datasets. Based on the results of this analysis, as well as on the presence of clade-specific indels in some of the actin-related proteins, we describe a novel ARP subfamily, dubbed ARP12, which is specific to heterokonts and related organisms...
October 23, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29031541/how-to-boost-marine-fungal-research-a-first-step-towards-a-multidisciplinary-approach-by-combining-molecular-fungal-ecology-and-natural-products-chemistry
#16
Marlis Reich, Antje Labes
Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production...
October 11, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28970064/cross-disciplinarity-in-the-advance-of-antarctic-ecosystem-research
#17
REVIEW
J Gutt, E Isla, A N Bertler, G E Bodeker, T J Bracegirdle, R D Cavanagh, J C Comiso, P Convey, V Cummings, R De Conto, D De Master, G di Prisco, F d'Ovidio, H J Griffiths, A L Khan, J López-Martínez, A E Murray, U N Nielsen, S Ott, A Post, Y Ropert-Coudert, T Saucède, R Scherer, S Schiaparelli, I R Schloss, C R Smith, J Stefels, C Stevens, J M Strugnell, S Trimborn, C Verde, E Verleyen, D H Wall, N G Wilson, J C Xavier
The biodiversity, ecosystem services and climate variability of the Antarctic continent and the Southern Ocean are major components of the whole Earth system. Antarctic ecosystems are driven more strongly by the physical environment than many other marine and terrestrial ecosystems. As a consequence, to understand ecological functioning, cross-disciplinary studies are especially important in Antarctic research. The conceptual study presented here is based on a workshop initiated by the Research Programme Antarctic Thresholds - Ecosystem Resilience and Adaptation of the Scientific Committee on Antarctic Research, which focussed on challenges in identifying and applying cross-disciplinary approaches in the Antarctic...
September 29, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28964713/circadian-signaling-in-the-northern-krill-meganyctiphanes-norvegica-in-silico-prediction-of-the-protein-components-of-a-putative-clock-system-using-a-publicly-accessible-transcriptome
#18
Andrew E Christie, Andy Yu, Micah G Pascual
The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn...
September 28, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28958500/using-rna-seq-to-determine-patterns-of-sex-bias-in-gene-expression-in-the-brain-of-the-sex-role-reversed-gulf-pipefish-syngnathus-scovelli
#19
Andria P Beal, F Douglas Martin, Matthew C Hale
Sex-bias in gene expression is a widespread mechanism for controlling the development of phenotypes that differ between males and females. Most studies on sex-bias in gene expression have focused on species that exhibit traditional sex-roles (male-male competition and female parental care). By contrast the Syngnathid fishes (sea horses, pipefish, and sea dragons) are a group of organisms where many species exhibit male brooding and sex-role reversal (female-female competition for mates and paternal parental care), and little is known about how patterns of sex-bias in gene expression vary in species with sex-role reversal...
September 22, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28919018/de-novo-transcriptome-assembly-of-the-calanoid-copepod-neocalanus-flemingeri-a-new-resource-for-emergence-from-diapause
#20
Vittoria Roncalli, Matthew C Cieslak, Stephanie A Sommer, Russell R Hopcroft, Petra H Lenz
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N...
September 14, 2017: Marine Genomics
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