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1.
J Child Custody ; 13(4): 250-258, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-28819347

RESUMEN

The present study examined how interparental violence, neighborhood violence, behavioral regulation during parental conflict, and age predicted beliefs about the acceptability of aggression and the acceptance of retaliation against an aggressive peer among youths. Participants were 110 families (mothers, fathers, and children) in which one or both parents met criteria for substance use disorder. Results of a bootstrapped path model revealed higher exposure to neighborhood violence predicted greater acceptability of general aggression, whereas higher father-to-mother violence perpetration predicted lower acceptability of general aggression. Higher exposure to neighborhood violence, behavioral dysregulation during parental conflict, and older child age predicted greater approval of retaliation toward an aggressive peer. Findings are interpreted as related to the cognitive-contextual framework.

2.
Environ Microbiol ; 17(10): 3481-99, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-24589037

RESUMEN

Understanding bacterioplankton community dynamics in coastal hypoxic environments is relevant to global biogeochemistry because coastal hypoxia is increasing worldwide. The temporal dynamics of bacterioplankton communities were analysed throughout the illuminated water column of Devil's Hole, Bermuda during the 6-week annual transition from a strongly stratified water column with suboxic and high-pCO2 bottom waters to a fully mixed and ventilated state during 2008. A suite of culture-independent methods provided a quantitative spatiotemporal characterization of bacterioplankton community changes, including both direct counts and rRNA gene sequencing. During stratification, the surface waters were dominated by the SAR11 clade of Alphaproteobacteria and the cyanobacterium Synechococcus. In the suboxic bottom waters, cells from the order Chlorobiales prevailed, with gene sequences indicating members of the genera Chlorobium and Prosthecochloris--anoxygenic photoautotrophs that utilize sulfide as a source of electrons for photosynthesis. Transitional zones of hypoxia also exhibited elevated levels of methane- and sulfur-oxidizing bacteria relative to the overlying waters. The abundance of both Thaumarcheota and Euryarcheota were elevated in the suboxic bottom waters (> 10(9) cells l(-1)). Following convective mixing, the entire water column returned to a community typical of oxygenated waters, with Euryarcheota only averaging 5% of cells, and Chlorobiales and Thaumarcheota absent.


Asunto(s)
Alphaproteobacteria/genética , Consorcios Microbianos/genética , Oxígeno/análisis , Plancton/genética , Agua de Mar/microbiología , Synechococcus/genética , Alphaproteobacteria/aislamiento & purificación , Bermudas , Dióxido de Carbono/análisis , Chlorobi/genética , Chlorobi/aislamiento & purificación , Euryarchaeota/aislamiento & purificación , Metano/metabolismo , Oxidación-Reducción , ARN Ribosómico , ARN Ribosómico 16S/genética , Azufre/metabolismo , Synechococcus/aislamiento & purificación
3.
Commun Earth Environ ; 5(1): 266, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38779128

RESUMEN

Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46 ± 24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.

4.
Nat Commun ; 15(1): 4089, 2024 May 14.
Artículo en Inglés | MEDLINE | ID: mdl-38744831

RESUMEN

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.


Asunto(s)
Bacteriófagos , Metagenoma , Metagenómica , Océanos y Mares , Agua de Mar , Metagenómica/métodos , Bacteriófagos/genética , Bacteriófagos/aislamiento & purificación , Bacteriófagos/clasificación , Agua de Mar/virología , Agua de Mar/microbiología , Metagenoma/genética , Genoma Viral/genética , Filogenia , Prochlorococcus/virología , Prochlorococcus/genética , Microbiota/genética , Bacterias/genética , Bacterias/virología , Bacterias/clasificación , Bacterias/aislamiento & purificación
5.
Environ Microbiol ; 15(5): 1452-63, 2013 May.
Artículo en Inglés | MEDLINE | ID: mdl-23279166

RESUMEN

Biogeographic patterns have been demonstrated for a wide range of microorganisms. Nevertheless, the biogeography of marine viruses has been slower to emerge. Here we investigate biogeographic patterns of marine cyanophages that infect Synechococcus sp. WH7803 across multiple spatial and temporal scales. We compared cyanophage myoviral communities from nine coastal sites in Southern New England (SNE), USA, one site in Long Island NY, and four sites from Bermuda's inshore waters by assaying cyanophage isolates using the myoviral g43 DNA polymerase gene. Cyanophage community composition varied temporally at each of the sites. Further, 6 years of sampling at one Narragansett Bay site revealed annual seasonal variations in community composition, driven by the seasonal reoccurrence of specific viral taxa. Although the four Bermuda communities were similar to one another, they were significantly different than the North American coastal communities, with almost no overlap of taxa between the two regions. Among the SNE sites, cyanophage community composition also varied significantly and was correlated with the body of water sampled (e.g. Narragansett Bay, Cape Cod Bay, Vineyard Sound), although here, the same viral taxa were found at multiple sites. This study demonstrates that marine cyanophages display striking seasonal and spatial biogeographic patterns.


Asunto(s)
Bacteriófagos/clasificación , Bacteriófagos/genética , Agua de Mar/virología , Synechococcus/virología , Organismos Acuáticos/clasificación , Organismos Acuáticos/genética , Bacteriófagos/aislamiento & purificación , Bermudas , Biodiversidad , ADN Polimerasa Dirigida por ADN/genética , Datos de Secuencia Molecular , New England , New York , Filogenia , Filogeografía , Estaciones del Año , Proteínas Virales/genética
6.
Biology (Basel) ; 12(2)2023 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-36829480

RESUMEN

Cephalopods' remarkable behavior and complex neurobiology make them valuable comparative model organisms, but studies aimed at enhancing welfare of captive cephalopods remain uncommon. Increasing regulation of cephalopods in research laboratories has resulted in growing interest in welfare-oriented refinements, including analgesia and anesthesia. Although general and local anesthesia in cephalopods have received limited prior study, there have been no studies of systemic analgesics in cephalopods to date. Here we show that analgesics from several different drug classes may be effective in E. berryi. Buprenorphine, ketorolac and dexmedetomidine, at doses similar to those used in fish, showed promising effects on baseline nociceptive thresholds, excitability of peripheral sensory nerves, and on behavioral responses to transient noxious stimulation. We found no evidence of positive effects of acetaminophen or ketamine administered at doses that are effective in vertebrates. Bioinformatic analyses suggested conserved candidate receptors for dexmedetomidine and ketorolac, but not buprenorphine. We also show that rapid general immersion anesthesia using a mix of MgCl2 and ethanol was successful in E. berryi at multiple age classes, similar to findings in other cephalopods. These data indicate that systemic analgesia and general anesthesia in Euprymna berryi are achievable welfare enhancing interventions, but further study and refinement is warranted.

7.
Front Microbiol ; 14: 1259014, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37869676

RESUMEN

Plastic waste accumulation in marine environments has complex, unintended impacts on ecology that cross levels of community organization. To measure succession in polyolefin-colonizing marine bacterial communities, an in situ time-series experiment was conducted in the oligotrophic coastal waters of the Bermuda Platform. Our goals were to identify polyolefin colonizing taxa and isolate bacterial cultures for future studies of the biochemistry of microbe-plastic interactions. HDPE, LDPE, PP, and glass coupons were incubated in surface seawater for 11 weeks and sampled at two-week intervals. 16S rDNA sequencing and ATR-FTIR/HIM were used to assess biofilm community structure and chemical changes in polymer surfaces. The dominant colonizing taxa were previously reported cosmopolitan colonizers of surfaces in marine environments, which were highly similar among the different plastic types. However, significant differences in rare community composition were observed between plastic types, potentially indicating specific interactions based on surface chemistry. Unexpectedly, a major transition in community composition occurred in all material treatments between days 42 and 56 (p < 0.01). Before the transition, Alteromonadaceae, Marinomonadaceae, Saccharospirillaceae, Vibrionaceae, Thalassospiraceae, and Flavobacteriaceae were the dominant colonizers. Following the transition, the relative abundance of these taxa declined, while Hyphomonadaceae, Rhodobacteraceae and Saprospiraceae increased. Over the course of the incubation, 8,641 colonizing taxa were observed, of which 25 were significantly enriched on specific polyolefins. Seven enriched taxa from families known to include hydrocarbon degraders (Hyphomonadaceae, Parvularculaceae and Rhodobacteraceae) and one n-alkane degrader (Ketobacter sp.). The ASVs that exhibited associations with specific polyolefins are targets of ongoing investigations aimed at retrieving plastic-degrading microbes in culture.

8.
Front Microbiol ; 14: 1287477, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-38179459

RESUMEN

Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 µm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 µmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 µm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.

9.
Bioorg Med Chem Lett ; 22(2): 901-6, 2012 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-22209458

RESUMEN

We describe here our attempts to optimise the human fatty acid amide hydrolase (FAAH) inhibition and physicochemical properties of our previously reported tetrasubstituted azetidine urea FAAH inhibitor, VER-156084. We describe the SAR of a series of analogues and conclude with the demonstration of in vivo dose-dependant FAAH inhibition in an anandamide-loading study in rats.


Asunto(s)
Amidohidrolasas/antagonistas & inhibidores , Azetidinas/farmacología , Inhibidores Enzimáticos/farmacología , Urea/farmacología , Amidohidrolasas/metabolismo , Animales , Azetidinas/síntesis química , Azetidinas/química , Inhibidores Enzimáticos del Citocromo P-450 , Sistema Enzimático del Citocromo P-450/metabolismo , Relación Dosis-Respuesta a Droga , Canal de Potasio ERG1 , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Canales de Potasio Éter-A-Go-Go/antagonistas & inhibidores , Humanos , Modelos Moleculares , Estructura Molecular , Ratas , Estereoisomerismo , Relación Estructura-Actividad , Urea/síntesis química , Urea/química
10.
ISME Commun ; 2(1): 116, 2022 Nov 19.
Artículo en Inglés | MEDLINE | ID: mdl-37938786

RESUMEN

SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.

11.
Front Microbiol ; 13: 833252, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35350629

RESUMEN

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016-2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.

12.
Environ Monit Assess ; 179(1-4): 309-24, 2011 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-20978839

RESUMEN

Bermuda is a densely populated coral 'atoll' located on a seamount in the mid-Atlantic (Sargasso Sea). There is no national sewerage system and the ∼20 × 10(6) L of sewage generated daily is disposed of via marine outfalls, cess pits/septic tanks underneath houses and through waste disposal (injection) wells. Gastrointestinal (GI) enterococci concentrations were measured in surface seawater samples collected monthly at multiple locations across the island over a 5-year period. According to the EU Bathing Water Directive microbial classification categories, 18 of the sites were in the 'excellent' category, four sites in the 'good', five sites were in the 'sufficient' and three sites in the 'poor' categories. One of the sites in the 'poor' category is beside a popular swimming beach. Between 20-30% of 58 sub tidal sediment samples collected from creeks, coves, bays, harbours and marinas in the Great Sound complex on the western side of Bermuda tested positive for the presence of the human specific bacterial biomarker Bacteroides (using culture-independent PCR-based methods) and for the faecal biomarker coprostanol (5ß-cholestan-3-ß-ol, which ranged in concentration from <0.05-0.77 mg kg( - 1). There was a significant statistical correlation between these two independent techniques for faecal contamination identification. Overall the microbial water quality and sedimentary biomarker surveys suggest sewage contamination in Bermuda was quite low compared with other published studies; nevertheless, several sewage contamination hotpots exist, and these could be attributed to discharge of raw sewage from house boats, from nearby sewage outfalls and leakage from septic tanks/cess pits.


Asunto(s)
Agua de Mar/microbiología , Aguas del Alcantarillado/análisis , Contaminantes del Agua/análisis , Bacteroides/crecimiento & desarrollo , Bacteroides/aislamiento & purificación , Bermudas , Colestanos/análisis , Arrecifes de Coral , Enterococcus/crecimiento & desarrollo , Enterococcus/aislamiento & purificación , Monitoreo del Ambiente , Sedimentos Geológicos/química , Sedimentos Geológicos/microbiología , Densidad de Población , Agua de Mar/química , Aguas del Alcantarillado/microbiología , Eliminación de Residuos Líquidos , Contaminación del Agua/análisis , Contaminación del Agua/estadística & datos numéricos
13.
Microbiol Resour Announc ; 10(7)2021 Feb 18.
Artículo en Inglés | MEDLINE | ID: mdl-33602731

RESUMEN

We present the genomes of two isolated bacteriophages infecting Pelagibacter ubique HTCC1062. Pelagibacter phage Mosig EXVC030M (Myoviridae) and Pelagibacter phage Lederberg EXVC029P (Podoviridae) were isolated by dilution-to-extinction culturing from the oxygen minimum zone at Devil's Hole (Harrington Sound, Bermuda).

14.
Org Biomol Chem ; 8(10): 2397-407, 2010 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-20448898

RESUMEN

CDK2 inhibitory structure-activity relationships have been explored for a range of 5-substituted O(4)-alkylpyrimidines. Variation of the 5-substituent in the 2,6-diaminopyrimidine series confirmed the 5-nitroso substituent as optimal, and showed that 5-formyl and 5-acetyl substituents were also tolerated at this position. A series of O(4)-alkyl-N(2)-aryl-5-substituted-6-aminopyrimidines revealed interesting structure-activity relationships. In the 5-nitroso series, the optimum O(4)-alkyl substituents were cyclohexylmethyl or sec-butyl, combined with a 2-sulfanilyl group. By contrast, in the N(2)-arylsulfonamido-5-formyl series, the cyclohexylmethyl compound showed relatively poor activity compared with the sec-butyl derivative (22j, (R)-4-(4-amino-6-sec-butoxy-5-formylpyrimidin-2-ylamino)benzenesulfonamide; CDK2 IC(50) = 0.8 nM). Similarly, in the N(2)-arylsulfonamido-5-(hydroxyiminomethyl) series the O(4)-sec-butyl substituent conferred greater potency than the cyclohexylmethyl (23c, (rac)-4-(4-amino-6-sec-butoxy-5-(hydroxyiminomethyl)pyrimidin-2-ylamino)benzenesulfonamide; CDK2 IC(50) = 7.4 nM). The 5-formyl derivatives show selectivity for CDK2 over other CDK family members, and are growth inhibitory in tumour cells (e.g. 22j, GI(50) = 0.57 microM).


Asunto(s)
Quinasa 2 Dependiente de la Ciclina/antagonistas & inhibidores , Oxígeno/química , Inhibidores de Proteínas Quinasas/síntesis química , Inhibidores de Proteínas Quinasas/farmacología , Pirimidinas/síntesis química , Pirimidinas/farmacología , Línea Celular Tumoral , Descubrimiento de Drogas , Humanos , Concentración 50 Inhibidora , Inhibidores de Proteínas Quinasas/química , Pirimidinas/química , Relación Estructura-Actividad
15.
Front Microbiol ; 11: 580397, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33117322

RESUMEN

Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using 13C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant 13C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant 13C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.

16.
mBio ; 11(1)2020 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-31911493

RESUMEN

It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.


Asunto(s)
Chloroflexi/enzimología , Chloroflexi/genética , Genoma Bacteriano , Metagenoma , Metagenómica , Familia de Multigenes , Biodiversidad , Biología Computacional/métodos , Redes y Vías Metabólicas , Metabolómica/métodos , Filogenia , Filogeografía
17.
PLoS Biol ; 4(11): e368, 2006 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-17090214

RESUMEN

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct "marine-ness" quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.


Asunto(s)
Genoma Viral , Agua de Mar/virología , Virus/genética , Bacteriófagos/aislamiento & purificación , Biodiversidad , ADN de Cadena Simple/aislamiento & purificación , Variación Genética , Biología Marina , Datos de Secuencia Molecular , Océanos y Mares , Filogenia , Sesgo de Selección , Manejo de Especímenes , Virus/clasificación , Virus/aislamiento & purificación
19.
PLoS One ; 12(3): e0173145, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28257422

RESUMEN

Factors that affect the removal of organic carbon by heterotrophic bacterioplankton can impact the rate and magnitude of organic carbon loss in the ocean through the conversion of a portion of consumed organic carbon to CO2. Through enhanced rates of consumption, surface bacterioplankton communities can also reduce the amount of dissolved organic carbon (DOC) available for export from the surface ocean. The present study investigated the direct effects of elevated pCO2 on bacterioplankton removal of several forms of DOC ranging from glucose to complex phytoplankton exudate and lysate, and naturally occurring DOC. Elevated pCO2 (1000-1500 ppm) enhanced both the rate and magnitude of organic carbon removal by bacterioplankton communities compared to low (pre-industrial and ambient) pCO2 (250 -~400 ppm). The increased removal was largely due to enhanced respiration, rather than enhanced production of bacterioplankton biomass. The results suggest that elevated pCO2 can increase DOC consumption and decrease bacterioplankton growth efficiency, ultimately decreasing the amount of DOC available for vertical export and increasing the production of CO2 in the surface ocean.


Asunto(s)
Dióxido de Carbono/metabolismo , Carbono/metabolismo , Ecosistema , Fitoplancton/metabolismo , Cianobacterias/metabolismo , Monitoreo del Ambiente , Humanos , Océanos y Mares , Agua de Mar/microbiología , Microbiología del Agua
20.
J Med Chem ; 60(6): 2271-2286, 2017 03 23.
Artículo en Inglés | MEDLINE | ID: mdl-28199108

RESUMEN

Libraries of nonpurified resorcinol amide derivatives were screened by surface plasmon resonance (SPR) to determine the binding dissociation constant (off-rate, kd) for compounds binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel off-rate measurements against HSP90 and application of structure-based drug design enabled rapid hit to lead progression in a program to identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization identified selective sub-100-nM inhibitors of the enzyme which significantly reduced phosphorylation of the E1α subunit in the PC3 cancer cell line in vitro.


Asunto(s)
Inhibidores de Proteínas Quinasas/química , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Adenosina Trifosfato/metabolismo , Línea Celular Tumoral , Diseño de Fármacos , Proteínas HSP90 de Choque Térmico/metabolismo , Humanos , Masculino , Modelos Moleculares , Fosforilación/efectos de los fármacos , Neoplasias de la Próstata/tratamiento farmacológico , Neoplasias de la Próstata/metabolismo , Isoformas de Proteínas/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Piruvato Deshidrogenasa Quinasa Acetil-Transferidora
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