Characterization of the Bioluminescent Symbionts from Ceratioids Collected in the Gulf of Mexico

Anglerfishes are easily one of the most popular deep-sea creatures due to their menacing appearance, extreme sexual dimorphism, parasitic mating approach, and eye catching bioluminescent lure. Unlike most bioluminescent fishes, which intrinsically generate light, female anglerfishes belonging to nine of the 11 families within the suborder Ceratioidei (deep-sea anglerfishes) have developed a symbiotic relationship with bioluminescent bacteria that are housed within the light organs. Previous molecular work had identified symbionts from two anglerfish species as novel and possibly unculturable taxa (Haygood et al., 1992), but nothing more has been revealed about the bioluminecent symbionts of ceratioids. As part of the Gulf of Mexico Research Initiative-funded DEEPEND project (Deependconsortium.org), the objective of this study is to characterize the escal microbiome of deep-sea anglerfishes and identify potential-symbiont taxa. A total of 36 anglerfish specimens were collected on DEEPEND cruises DP01 through DP04. These specimens consist of adult and larval individuals belonging to six of the families with the suborder Ceratioidei: Ceratiidae (n=22), Oneirodidae (n=7), Linophrynidae (n=3), Melanocetidae (n=2), Centrophrynidae (n=1), Melanocetidae (n=2), Gigantactinidae (n=1). DNA was extracted from esca, skin, fin, gill, gut, and caruncle tissues, as well as seawater. High-throughput sequencing of the 16S rRNA hypervariable V4 region was carried out using the Illumina MiSeq. Sequencing revealed five potential bioluminescent-symbiont taxa (OTU IDs: 9129, 9131, 160210, 523223, and 939811), which had the greatest relative abundance (25.2% - 98.7%) within 12 of 21 adult specimens. These taxa belong to the family Vibrionaceae and were found at greater than 10% relative abundance in the escal samples of adult anglerfishes belonging to the Ceratiidae and Melanocetidae families, but they were not found in high abundance in larval individuals of the same families. Sequencing of larval samples revealed five potential bioluminescent-symbiont taxa (OTU IDs: 136178, 176420, 523223, 837366, 939811) which were of greatest relative abundance (8.1%-67.1%) within nine of 13 specimens. Also members of the family Vibrionaceae, these taxa were found in high abundance in larval anglerfishes belonging to the Oneirodidae, Linophrynidae, Gigantactinidae, and Ceratiidae families. This study is the first to to examine the bioluminescent symbionts from seven different ceratioid families

Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes

Diverse marine fish and squid form symbiotic associations with extracellular bioluminescent bacteria. These symbionts are typically free-living bacteria with large genomes, but one known lineage of symbionts has undergone genomic reduction and evolution of host dependence. It is not known why distinct evolutionary trajectories have occurred among different luminous symbionts, and not all known lineages previously had genome sequences available. In order to better understand patterns of evolution across diverse bioluminescent symbionts, we de novo sequenced the genomes of bacteria from a poorly studied interaction, the extracellular symbionts from the “lures” of deep-sea ceratioid anglerfishes. Deep-sea anglerfish symbiont genomes are reduced in size by about 50% compared to free-living relatives. They show a striking convergence of genome reduction and loss of metabolic capabilities with a distinct lineage of obligately host-dependent luminous symbionts. These losses include reductions in amino acid synthesis pathways and abilities to utilize diverse sugars. However, the symbiont genomes have retained a number of categories of genes predicted to be useful only outside the host, such as those involved in chemotaxis and motility, suggesting that they may persist in the environment. These genomes contain very high numbers of pseudogenes and show massive expansions of transposable elements, with transposases accounting for 28 and 31% of coding sequences in the symbiont genomes. Transposon expansions appear to have occurred at different times in each symbiont lineage, indicating either independent evolutions of reduction or symbiont replacement. These results suggest ongoing genomic reduction in extracellular luminous symbionts that is facilitated by transposon proliferations

Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment

Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and that these bacteria have undergone extreme genome reduction although they are not vertically transmitted

Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid anglerfishes of the gulf of mexico

The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities (‘microbiomes’) and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA. Transmission Electron Microscopy was used to characterize the location of symbionts in adult light organs (esca). Whole larval microbiomes, and adult skin and gut microbiomes, were dominated by bacteria in the genera Moritella and Pseudoalteromonas genera. 16S rDNA sequencing results from adult fishes corroborate the previously published identity of ceratioid bioluminescent symbionts and support findings that these symbionts do not consistently exhibit host specificity at the host family level. Bioluminescent symbiont amplicon sequence variants (ASVs) were absent from larval ceratioid samples, but were found at all depths in the seawater, with a highest abundance found at mesopelagic depths. As adults spend the majority of their lives in the meso and bathypelagic, the trend in symbiont abundance is consistent with their life history. These findings support the hypothesis that bioluminescent symbionts are not present throughout host development, and that ceratioids acquire their bioluminescent symbionts from the environment

Performance of ICD‐10‐CM diagnosis codes for identifying children with Sickle Cell Anemia

ObjectiveTo develop, test, and validate the performance of ICD‐10‐CM claims‐based case definitions for identifying children with sickle cell anemia (SCA).Data SourcesMedicaid administrative claims (2016) for children <18 years with potential SCA (any D57x diagnosis code) and newborn screening records from Michigan and New York State.Study DesignThis study is a secondary data analysis.Data Collection/Extraction MethodsUsing specific SCA‐related (D5700, D5701, and D5702) and nonspecific (D571) diagnosis codes, 23 SCA case definitions were applied to Michigan Medicaid claims (2016) to identify children with SCA. Measures of performance (sensitivity, specificity, area under the ROC curve) were calculated using newborn screening results as the gold standard. A parallel analysis was conducted using New York State Medicaid claims and newborn screening data.Principal FindingsIn Michigan Medicaid, 1597 children had ≥1 D57x claim; 280 (18 percent) were diagnosed with SCA. Measures of performance varied, with sensitivities from 0.02 to 0.97 and specificities from 0.88 to 1.0. The case definition of ≥1 outpatient visit with a SCA‐related or D571 code had the highest area under the ROC curve, with a sensitivity of 95 percent and specificity of 92 percent. The same definition also had the highest performance in New York Medicaid (n = 2454), with a sensitivity of 94 percent and specificity of 86 percent.ConclusionsChildren with SCA can be accurately identified in administrative claims using this straightforward case definition. This methodology can be used to monitor trends and use of health services after transition to ICD‐10‐CM.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154614/1/hesr13257.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154614/2/hesr13257_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154614/3/hesr13257-sup-0001-Authormatrix.pd

Rab11-FIP1C and Rab14 Direct Plasma Membrane Sorting and Particle Incorporation of the HIV-1 Envelope Glycoprotein Complex

The incorporation of the envelope glycoprotein complex (Env) onto the developing particle is a crucial step in the HIV-1 lifecycle. The long cytoplasmic tail (CT) of Env is required for the incorporation of Env onto HIV particles in T cells and macrophages. Here we identify the Rab11a-FIP1C/RCP protein as an essential cofactor for HIV-1 Env incorporation onto particles in relevant human cells. Depletion of FIP1C reduced Env incorporation in a cytoplasmic tail-dependent manner, and was rescued by replenishment of FIP1C. FIP1C was redistributed out of the endosomal recycling complex to the plasma membrane by wild type Env protein but not by CT-truncated Env. Rab14 was required for HIV-1 Env incorporation, and FIP1C mutants incapable of binding Rab14 failed to rescue Env incorporation. Expression of FIP1C and Rab14 led to an enhancement of Env incorporation, indicating that these trafficking factors are normally limiting for CT-dependent Env incorporation onto particles. These findings support a model for HIV-1 Env incorporation in which specific targeting to the particle assembly microdomain on the plasma membrane is mediated by FIP1C and Rab14. © 2013 Qi et al.Link_to_subscribed_fulltex

Complete bacterial symbiont genome sequences from anglerfish Cryptopsaras couesii and Melanocetus johnsonii

These are the complete bacterial symbiont genome sequences from anglerfish Cryptopsaras couesii (individual CC26) and one individual Melanocetus johnsonii. These data were generated and analyzed by the laboratory of Dr Tory Hendry (Cornell University). The full sequences of two symbiotic bacterial genomes have been submitted to public DDBJ/ENA/GenBank repositories under the accessions CP020660- CP020663 (CC26 Cryptopsaras couesii) and NBYY01000001-NBYY01000039 (Melanocetus johnsonii). The total genome size for each of the symbiont species is about 2-2.6 Mb

Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes

Diverse marine fish and squid form symbiotic associations with extracellular bioluminescent bacteria. These symbionts are typically free-living bacteria with large genomes, but one known lineage of symbionts has undergone genomic reduction and evolution of host dependence. It is not known why distinct evolutionary trajectories have occurred among different luminous symbionts, and not all known lineages previously had genome sequences available. In order to better understand patterns of evolution across diverse bioluminescent symbionts, we de novo sequenced the genomes of bacteria from a poorly studied interaction, the extracellular symbionts from the “lures” of deep-sea ceratioid anglerfishes. Deep-sea anglerfish symbiont genomes are reduced in size by about 50% compared to free-living relatives. They show a striking convergence of genome reduction and loss of metabolic capabilities with a distinct lineage of obligately host-dependent luminous symbionts. These losses include reductions in amino acid synthesis pathways and abilities to utilize diverse sugars. However, the symbiont genomes have retained a number of categories of genes predicted to be useful only outside the host, such as those involved in chemotaxis and motility, suggesting that they may persist in the environment. These genomes contain very high numbers of pseudogenes and show massive expansions of transposable elements, with transposases accounting for 28 and 31% of coding sequences in the symbiont genomes. Transposon expansions appear to have occurred at different times in each symbiont lineage, indicating either independent evolutions of reduction or symbiont replacement. These results suggest ongoing genomic reduction in extracellular luminous symbionts that is facilitated by transposon proliferations.Many female deep-sea anglerfishes possess a “lure” containing luminous bacterial symbionts. Here we show that unlike most luminous symbionts, these bacteria are undergoing an evolutionary transition toward small genomes with limited metabolic capabilities. Comparative analyses of the symbiont genomes indicate that this transition is ongoing and facilitated by transposon expansions. This transition may have occurred independently in different symbiont lineages, although it is unclear why. Genomic reduction is common in bacteria that only live within host cells but less common in bacteria that, like anglerfish symbionts, live outside host cells. Since multiple evolutions of genomic reduction have occurred convergently in luminous bacteria, they make a useful system with which to understand patterns of genome evolution in extracellular symbionts. This work demonstrates that ecological factors other than an intracellular lifestyle can lead to dramatic gene loss and evolutionary changes and that transposon expansions may play important roles in this process

Factors associated with interhospital transfer of children with respiratory failure from level II to level I pediatric intensive care units

Purpose: Of all sources of admission to level I pediatric intensive care units (PICUs), interhospital transfer admissions from level II PICUs carry the highest mortality and resource use burden. We sought to investigate factors associated with transfer of children with respiratory failure from level II to level I PICUs. Methods: A case-control study was conducted among children with respiratory failure admitted to 6 level II PICUs between January 1, 1997, and December 31, 2007, with frequency matching of 466 nontransferred children (controls) to 187 transferred children (cases). Results: Among 653 children, transferred children were younger and had more comorbidities. After multivariable analysis, transferred children were more likely to have comorbidities (odds ratio [OR], 2.02; 95% confidence interval [CI], 1.36-2.98) and receive escalated care including high-frequency ventilation (OR, 2.57; 95% CI, 1.04-6.37) and surfactant therapy (OR, 5.33; 95% CI, 1.35-21.0). Conclusions: The study identified patient-level and process-of-care factors associated with transfer from level II to level I PICUs. These findings highlight the influence of escalated care on transfer decision making for critically ill children in respiratory failure

Factors associated with interhospital transfer of children with respiratory failure from level II to level I pediatric intensive care units

Purpose: Of all sources of admission to level I pediatric intensive care units (PICUs), interhospital transfer admissions from level II PICUs carry the highest mortality and resource use burden. We sought to investigate factors associated with transfer of children with respiratory failure from level II to level I PICUs. Methods: A case-control study was conducted among children with respiratory failure admitted to 6 level II PICUs between January 1, 1997, and December 31, 2007, with frequency matching of 466 nontransferred children (controls) to 187 transferred children (cases). Results: Among 653 children, transferred children were younger and had more comorbidities. After multivariable analysis, transferred children were more likely to have comorbidities (odds ratio [OR], 2.02; 95% confidence interval [CI], 1.36-2.98) and receive escalated care including high-frequency ventilation (OR, 2.57; 95% CI, 1.04-6.37) and surfactant therapy (OR, 5.33; 95% CI, 1.35-21.0). Conclusions: The study identified patient-level and process-of-care factors associated with transfer from level II to level I PICUs. These findings highlight the influence of escalated care on transfer decision making for critically ill children in respiratory failure