Investigation of vitamin B12 concentrations and tissue distributions in larval and adult Pacific oysters and related bivalves

itamin B 12 (B 12 ) is an essential micronutrient for all animals, but is not present in plants and is produced de novo only by bacteria or archaea. Accordingly, humans must derive required B 12 from eating animal products or vitamin supplements, as deficiencies can lead to severe health issues including neuropathy. An often overlooked source in the human diet of B 12 is shellfish, in particular bivalves, which have significantly higher levels of B 12 than other animal sources, including all vertebrate meats. Origins and key metabolic processes involving B 12 in bivalves remain largely unknown, despite the exceptionally high levels. In this study, we examined in several Australian bivalve species, hypotheses concerning B 12 utilisation and uptake through diet or microorganism symbiosis. Vitamin B 12 is not distributed evenly across different tissues types of the Pacific oyster, the commercial scallop and Goolwa cockle (pipi), with higher accumulation in the oyster adductor muscle and gill, and mantle and syphons of the Goolwa cockle. Oyster larvae before first feeding already contained high amount of B 12 ; however, a significant decrease in B 12 concentration post metamorphosis indicates a higher utilisation of B 12 during this life event. We demonstrated that microalgal feed can be supplemented with B 12 , resulting in an enriched feed, but this did not result in an increase in larval B 12 concentrations when oyster larvae were fed with this diet relative to controls, thus supporting the theory that a B 12 producing microbiome within bivalves was the potential source of B 12 rather than feed. However, B 12 concentrations in the digestive tract of adult oysters were low compared to other tissue types, which might challenge this theory, at least in adults. Our findings provide insight into B 12 uptake and function in bivalve species, which will aid the promotion of bivalves as suitable B 12 source for humans as well as provide crucial information to the aquaculture industry in relation to optimisation of vitamin supplementation in bivalve hatchery production.

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Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696)

Genome Announcements ◽

10.1128/genomea.00731-17 ◽

2017 ◽

Vol 5 (32) ◽

Cited By ~ 1

Author(s):

Chang-Young Hong ◽

Su-Yeon Lee ◽

Sun-Hwa Ryu ◽

Sung-Suk Lee ◽

Myungkil Kim

Keyword(s):

Phanerochaete Chrysosporium ◽

De Novo ◽

Gene Annotation ◽

Draft Genome ◽

Whole Genome ◽

Content Type ◽

Protein Encoding ◽

Crucial Information ◽

And Function ◽

Encoding Genes

ABSTRACT Phanerochaete chrysosporium (ATCC 20696) has a catabolic ability to degrade lignin. Here, we report whole-genome sequencing used to identify genes related to lignin modification. We determined the 39-Mb draft genome sequence of this fungus, comprising 13,560 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes.

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Pathologies in commercial bivalve species from Santa Catarina State, southern Brazil

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315411001007 ◽

2011 ◽

Vol 92 (3) ◽

pp. 571-579 ◽

Cited By ~ 13

Author(s):

Patricia Mirella da Silva ◽

Aimê Rachel Magenta Magalhães ◽

Margherita Anna Barracco

Keyword(s):

Bivalve Species ◽

Southern Brazil ◽

Chain Reaction ◽

Santa Catarina ◽

Negative Results ◽

Pacific Oysters ◽

The Pacific ◽

High Prevalence ◽

Polymerase Chain ◽

Santa Catarina State

The State of Santa Catarina in southern Brazil is the most important Brazilian producer region. The Pacific oysters Crassostrea gigas and the brown mussels Perna perna are the main species currently produced. The occurrence and impact of parasites on bivalves from natural or culture populations from Brazil are still poorly studied. This work describes several diseases, parasites and commensals from four edible bivalve species, from cultured and exploited stocks, from five sites at Santa Catarina State. Unspecific histopathological symptoms of stress, parasites and commensals were found, including viral gametocytic hypertrophy and rickettsia-like organisms with very low prevalences; the protozoan Nematopsis sp. with high prevalence and, ovarian parasites with low prevalences; and, diverse metazoans, such as turbellarian, sporocysts and metacercariae of trematodes, metacestoda larvae and spionid polychaete. Ray's fluid thioglycollate medium assays for detection of Perkinsus spp. did not detect any infected bivalves. Polymerase chain reaction assays for Marteiliodies chungmuensis in oysters with ovarian lesions produced negative results.

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riboCIRC: a comprehensive database of translatable circRNAs

Genome Biology ◽

10.1186/s13059-021-02300-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Huihui Li ◽

Mingzhe Xie ◽

Yan Wang ◽

Ludong Yang ◽

Zhi Xie ◽

...

Keyword(s):

De Novo ◽

Species Conservation ◽

Structure And Function ◽

Research Community ◽

Genome Browser ◽

Valuable Resource ◽

Sequence Structure ◽

A Genome ◽

Context Specific ◽

And Function

AbstractriboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com.

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Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park

Applied and Environmental Microbiology ◽

10.1128/aem.01095-15 ◽

2015 ◽

Vol 81 (17) ◽

pp. 5907-5916 ◽

Cited By ~ 13

Author(s):

Z. J. Jay ◽

J. P. Beam ◽

A. Dohnalkova ◽

R. Lohmayer ◽

B. Bodle ◽

...

Keyword(s):

Yellowstone National Park ◽

National Park ◽

Elemental Sulfur ◽

De Novo ◽

Hot Spring ◽

Content Type ◽

Physiological Attributes ◽

And Function ◽

Metagenome Sequence

ABSTRACTThermoproteales(phylumCrenarchaeota) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolatePyrobaculum yellowstonensisstrain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurringin situ. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for thede novosynthesis of nearly all required cofactors and metabolites were identified. The comparative genomics ofP. yellowstonensisand the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) toin situpopulations. The physiological attributes and metabolic capabilities ofP. yellowstonensisprovide an important foundation for developing an understanding of the distribution and function of these populations in YNP.

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Steroidogenic Factor-1 (SF-1)-Driven Differentiation of Murine Embryonic Stem (ES) Cells into a Gonadal Lineage

Endocrinology ◽

10.1210/en.2011-0219 ◽

2011 ◽

Vol 152 (7) ◽

pp. 2870-2882 ◽

Cited By ~ 24

Author(s):

Unmesh Jadhav ◽

J. Larry Jameson

Keyword(s):

Target Genes ◽

De Novo ◽

Embryoid Body ◽

Es Cells ◽

Embryonic Stem ◽

Cell Lineage ◽

Culture Conditions ◽

Steroidogenic Factor 1 ◽

Lineage Differentiation ◽

And Function

Steroidogenic factor 1 (SF-1) is essential for the development and function of steroidogenic tissues. Stable incorporation of SF-1 into embryonic stem cells (SF-1-ES cells) has been shown to prime the cells for steroidogenesis. When provided with exogenous cholesterol substrate, and after treatment with retinoic acid and cAMP, SF-1-ES cells produce progesterone but do not produce other steroids such as cortisol, estradiol, or testosterone. In this study, we explored culture conditions that optimize SF-1-mediated differentiation of ES cells into defined steroidogenic lineages. When embryoid body formation was used to facilitate cell lineage differentiation, SF-1-ES cells were found to be restricted in their differentiation, with fewer cells entering neuronal pathways and a larger fraction entering the steroidogenic lineage. Among the differentiation protocols tested, leukemia inhibitory factor (LIF) removal, followed by prolonged cAMP treatment was most efficacious for inducing steroidogenesis in SF-1-ES cells. In this protocol, a subset of SF-1-ES cells survives after LIF withdrawal, undergoes morphologic differentiation, and recovers proliferative capacity. These cells are characterized by induction of steroidogenic enzyme genes, use of de novo cholesterol, and production of multiple steroids including estradiol and testosterone. Microarray studies identified additional pathways associated with SF-1 mediated differentiation. Using biotinylated SF-1 in chromatin immunoprecipitation assays, SF-1 was shown to bind directly to multiple target genes, with induction of binding to some targets after steroidogenic treatment. These studies indicate that SF-1 expression, followed by LIF removal and treatment with cAMP drives ES cells into a steroidogenic pathway characteristic of gonadal steroid-producing cells.

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A disease-associated frameshift mutation in caveolin-1 disrupts caveolae formation and function through introduction of a de novo ER retention signal

Molecular Biology of the Cell ◽

10.1091/mbc.e17-06-0421 ◽

2017 ◽

Vol 28 (22) ◽

pp. 3095-3111 ◽

Cited By ~ 11

Author(s):

Courtney A. Copeland ◽

Bing Han ◽

Ajit Tiwari ◽

Eric D. Austin ◽

James E. Loyd ◽

...

Keyword(s):

Frameshift Mutation ◽

De Novo ◽

Dominant Negative ◽

Caveolin 1 ◽

Protein Levels ◽

C Terminus ◽

Er Retention ◽

And Function ◽

Er Retention Signal ◽

Retention Signal

Caveolin-1 (CAV1) is an essential component of caveolae and is implicated in numerous physiological processes. Recent studies have identified heterozygous mutations in the CAV1 gene in patients with pulmonary arterial hypertension (PAH), but the mechanisms by which these mutations impact caveolae assembly and contribute to disease remain unclear. To address this question, we examined the consequences of a familial PAH-associated frameshift mutation in CAV1, P158PfsX22, on caveolae assembly and function. We show that C-terminus of the CAV1 P158 protein contains a functional ER-retention signal that inhibits ER exit and caveolae formation and accelerates CAV1 turnover in Cav1–/– MEFs. Moreover, when coexpressed with wild-type (WT) CAV1 in Cav1–/– MEFs, CAV1-P158 functions as a dominant negative by partially disrupting WT CAV1 trafficking. In patient skin fibroblasts, CAV1 and caveolar accessory protein levels are reduced, fewer caveolae are observed, and CAV1 complexes exhibit biochemical abnormalities. Patient fibroblasts also exhibit decreased resistance to a hypo-osmotic challenge, suggesting the function of caveolae as membrane reservoir is compromised. We conclude that the P158PfsX22 frameshift introduces a gain of function that gives rise to a dominant negative form of CAV1, defining a new mechanism by which disease-associated mutations in CAV1 impair caveolae assembly.

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A de novo approach to disentangle partner identity and function in holobiont systems

10.1101/221424 ◽

2017 ◽

Author(s):

Arnaud Meng ◽

Camille Marchet ◽

Erwan Corre ◽

Pierre Peterlongo ◽

Adriana Alberti ◽

...

Keyword(s):

Functional Diversity ◽

De Novo ◽

Model Organisms ◽

Symbiotic Association ◽

Proof Of Concept ◽

Short Read ◽

Symbiotic Associations ◽

Functional Annotations ◽

And Function ◽

Similarity Method

AbstractBackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.ResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner’s transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.

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Glial Hedgehog and lipid metabolism regulate neural stem cell proliferation in Drosophila

10.1101/2020.05.18.100990 ◽

2020 ◽

Author(s):

Qian Dong ◽

Michael Zavortink ◽

Francesca Froldi ◽

Sofya Golenkina ◽

Tammy Lam ◽

...

Keyword(s):

Lipid Metabolism ◽

Cell Cycle Progression ◽

De Novo ◽

De Novo Lipogenesis ◽

Post Translational Modification ◽

Final Size ◽

Neural Lineage ◽

Signalling Molecule ◽

Lipid Metabolism Genes ◽

And Function

AbstractThe final size and function of the adult central nervous system (CNS) is determined by neuronal lineages generated by neural stem cells (NSCs) in the developing brain. In Drosophila, NSCs called neuroblasts (NBs) reside within a specialised microenvironment called the glial niche. Here, we explore non-autonomous glial regulation of NB proliferation. We show that lipid droplets (LDs) which reside within the glial niche are closely associated with the signalling molecule Hedgehog (Hh). Under physiological conditions, cortex glial Hh is autonomously required to sustain niche chamber formation, and non-autonomously restrained to prevent ectopic Hh signalling in the NBs. In the context of cortex glial overgrowth, induced by Fibroblast Growth Factor (FGF) activation, Hh and lipid storage regulators Lsd-2 and Fasn1 were upregulated, resulting in activation of Hh signalling in the NBs; which in turn disrupted NB cell cycle progression and reduced neuronal production. We show that the LD regulator Lsd-2 modulates Hh’s ability to signal to NBs, and de novo lipogenesis gene Fasn1 regulates Hh post-translational modification via palmitoylation. Together, our data suggest that the glial niche non-autonomously regulates NB proliferation and neural lineage size via Hh signaling that is modulated by lipid metabolism genes.

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Distribution, Condition and Gonad Maturity of the Invasive Pacific Oysters (Crassostrea Gigas, Thunberg 1793) in Cimanuk Delta, Indramayu, West Java, Indonesia

Omni-Akuatika ◽

10.20884/1.oa.2017.13.2.237 ◽

2017 ◽

Vol 13 (2) ◽

Cited By ~ 1

Author(s):

Selia Hermawati ◽

Sulistiono Sulistiono ◽

Agustinus M Samosir

Keyword(s):

Distribution Pattern ◽

Crassostrea Gigas ◽

Brackish Water ◽

Pacific Oyster ◽

Condition Factor ◽

Maturity Stage ◽

West Java ◽

Gonad Maturity ◽

Pacific Oysters ◽

The Pacific

Pacific oyster (Crassostrea gigas) is an invasive species which is able to adapt a wide range of environmental conditions. The study was conducted from August to October 2014. Objective of this study was to asses the distribution pattern, condition and gonad maturity length (Lm 50%) of the Pacific oysters in mangrove ecosystem of Cimanuk Delta, Indramayu, West Java, Indonesia. This study was conducted in two adjacent areas: Pabean Ilir and Pagirikan subdeltas. The oysters were collected from the estuary, brackish water ponds and the coastal flat, and observed for their abundance, total length (mm) and weight (g). Morphological and histological methods were used to estimate the gonad maturity stage. Analysis were carried out to estimate distribution pattern and condition factor. According to the study, the Pacific oyster distribution pattern was clumped. The condition factor of the oyster was higher in the brackish water pond and estuary than in the coastal flat. The Pacific oyster was found in gonad maturity stage (GMS) I – IV. The oyster was hermaprodit protandry and had length maturity (Lm 50%) of 47,46-48,43 mm (male) and 75,27-75,50 mm (female).

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