Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium

Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade) under four element limitation regimes (C, N, P, and S). Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to sixfold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometry in R. pomeroyi may have implications for global carbon cycling if extendable to other heterotrophic bacteria. Strong homeostatic responses to N limitation by marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean

Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011

Background: The Amazon River runs nearly 6500 km across the South American continent before emptying into the western tropical North Atlantic Ocean. In terms of both volume and watershed area, it is the world’s largest riverine system, affecting elemental cycling on a global scale. Results: A quantitative inventory of genes and transcripts benchmarked with internal standards was obtained at five stations in the lower Amazon River during May 2011. At each station, metagenomes and metatranscriptomes were obtained in duplicate for two microbial size fractions (free-living, 0.2 to 2.0 μm; particle-associated, 2.0 to 297 μm) using 150 × 150 paired-end Illumina sequencing. Forty eight sample datasets were obtained, averaging 15 × 10⁶ potential protein-encoding reads each (730 × 10⁶ total). Prokaryotic metagenomes and metatranscriptomes were dominated by members of the phyla Actinobacteria, Planctomycetes, Betaproteobacteria, Verrucomicrobia, Nitrospirae, and Acidobacteria. The actinobacterium SCGC AAA027-L06 reference genome recruited the greatest number of reads overall, with this single bin contributing an average of 50 billion genes and 500 million transcripts per liter of river water. Several dominant taxa were unevenly distributed between the free-living and particle-associated size fractions, such as a particle-associated bias for reads binning to planctomycete Schlesneria paludicola and a free-living bias for actinobacterium SCGC AAA027-L06. Gene expression ratios (transcripts to gene copy ratio) increased downstream from Óbidos to Macapá and Belém, indicating higher per cell activity of Amazon River bacteria and archaea as river water approached the ocean. Conclusion: This inventory of riverine microbial genes and transcripts, benchmarked with internal standards for full quantitation, provides an unparalleled window into microbial taxa and functions in the globally important Amazon River ecosystem.Supporting Information: Sequences from this May 2011 Amazon Continuum study are available from NCBI under accession numbers SRP039390 (metagenomes) and SRP037995 (metatranscriptomes). The NCBI sequences are fastq files from which internal standard sequences (metagenomes and metatranscriptomes) and rRNA sequences (metatranscriptomes only) have been removed prior to deposition. Metadata accompanying the omics datasets are provided in Additional file 2. ANACONDAS and ROCA project data are also available at the BCO-DMO data repository (http://www.bco-dmo.org/project/2097)

Cryptic carbon and sulfur cycling between surface ocean plankton

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 453-457, doi:10.1073/pnas.1413137112 .About half the carbon fixed by phytoplankton in the ocean is taken up and metabolized by marine bacteria, a transfer that is mediated through the seawater dissolved organic carbon (DOC) pool. The chemical complexity of marine DOC, along with a poor understanding of which compounds form the basis of trophic interactions between bacteria and phytoplankton, have impeded efforts to identify key currencies of this carbon cycle link. Here, we used transcriptional patterns in a bacterial-diatom model system based on vitamin B12 auxotrophy as a sensitive assay for metabolite exchange between marine plankton. The most highly upregulated genes (up to 374-fold) by a marine Roseobacter clade bacterium when co-cultured with the diatom Thalassiosira pseudonana were those encoding the transport and catabolism of 2,3- dihydroxypropane-1-sulfonate (DHPS). This compound has no currently recognized role in the marine microbial food web. As the genes for DHPS catabolism have limited distribution among bacterial taxa, T. pseudonana may use this novel sulfonate for targeted feeding of beneficial associates. Indeed, DHPS was both a major component of the T. pseudonana cytosol and an abundant microbial metabolite in a diatom bloom in the eastern North Pacific Ocean. Moreover, transcript analysis of the North Pacific samples provided evidence of DHPS catabolism by Roseobacter populations. Other such biogeochemically important metabolites may be common in the ocean but difficult to discriminate against the complex chemical background of seawater. Bacterial transformation of this diatom-derived sulfonate represents a new and likely sizeable link in both the marine carbon and sulfur cycles.This research was partially funded by NSF grants OCE-1356010 to M.A.M., OCE-1205233 to E.V.A., OCE-0928424 to E.B.K., and OCE-1233964 to S.R.C., and by the Gordon and Betty Moore Foundation grants 538.01 to M.A.M. and 537.01 to E.V.A.2015-06-2

Optimal Parameterized Policies for Resource Allocation in Communication Networks

The problem of finding optimal parameterized feedback policies for dynamic bandwidth allocation in communication networks is studied. We consider a queueing model with two queues to which traffic from different competing flows arrive. The queue length at the buffers is observed every T instants of time, on the basis of which a decision on the amount of bandwidth to be allocated to each buffer for the next T instants is made. We consider two different classes of multilevel closed-loop feedback policies for the system and use a two-timescale simultaneous perturbation stochastic approximation (SPSA) algorithm to find optimal policies within each prescribed class. We study the performance of the proposed algorithm on a numerical setting and show performance comparisons of the two optimal multilevel closedloop policies with optimal open loop policies. We observe that closed loop policies of Class B that tune parameters for both the queues and do not have the constraint that the entire bandwidth be used at each instant exhibit the best results overall as they offer greater flexibility in parameter tuning. Index Terms — Resource allocation, dynamic bandwidth allocation in communication networks, two-timescale SPSA algorithm, optimal parameterized policies. I

Synthesis of some newer indolyl-thiadiazolyl-pyrazolines and indolyl-oxadiazolyl-pyrazolines as potential anti-inflammatory agents

2647-2654Some new l-acetyl-5-substitutedaryl-3-[5 '-(3"-indolylmethyl)-2'-amino-1',3',4'-thiadiazol-2' N-yl]-2-pyrazolines 6a-6c and 1-acetyl-5-substitutedaryl-3-[5'-(3"-indolylmethyl)-2'-amino-1' ,3' ,4'-oxadiazol-2' N-yl]-2-pyrazolines 6'a-6'e have been synthesized by 5-(3'-indolymethyl)- 1,3,4-thiadiazolyl-2-aminosubstitutedchalkones 5a-5e and 5-(3'-indolylmethyl)-1,3,4-oxadiazolyl-2-aminosubstitutedchalkones 5'a-5'e, respectively. All these compounds of the present series have been screened for their anti-inflammatory activity. Compounds 6c and 6'c are found to be most active compound of this series, which show 47.6% and 49.0% inflammation inhibitory activity at a dose of 50 mg/kg p.o., while standard drug phenylbutazone exhibit 45.6% anti-inflammatory activity at same dose. The structure of these compounds has been illustrated by IR and 1H NMR spectra

An algorithm for dynamic optimal bandwidth allocation in communication networks

We study the problem of optimal bandwidth allocation in communication networks. We consider a queueing model with two queues to which traffic from different competing flows arrive. The queue length at the buffers is observed every T instants of time, on the basis of which a decision on the amount of bandwidth to be allocated to each buffer for the next T instants is made. We consider a class of closed-loop feedback policies for the system and use a twotimescale simultaneous perturbation stochastic approximation(SPSA) algorithm to find an optimal policy within the prescribed class. We study the performance of the proposed algorithm on a numerical setting. Our algorithm is found to exhibit good performance

Synthesis and pesticidal activities of some substituted pyridine derivatives

1557-1563Several pyridinylthiazolylazetidinones 4a-d, pyridinylthiazoly­thia­zolidinones 5a-d and pyridinylthiazolylformazans 6a-d have been prepared from pyridinylthiazolylarylidines 3a-d. These compounds have been evaluated for insecticidal, anti-fungal and anti-bacterial activities. Compound 2-[2'-(3"-chloro-2"-oxo-4"-o-hydroxyphenyl-1"-azetidinyl)-1',3'-thiazol-4'-yl) aminopyridine 4c has been found to exhibit potential insecticidal and anti-fungal properties.The structure of these compounds has been elucidated by elemental (C, H, N) and spectral (IR, 1H NMR and mass) analyses. All the compounds except 3a-d and 6c, 6d show antibacterial activity

Synthesis and antimicrobial activity of thiazolidinone norfloxacin hybrids

1496-1503A new series of 1-ethyl-6-fluoro-7-piperazinyl-4-oxo-3-(substitutedarylidinylcarboxy-hydrazido)quinolines 3-7 and 1-ethyl-6-fluoro-7-piperazinyl-4-oxo-3-(2¢-substitutedaryl-4¢-oxo-1¢,3¢-thiazolidin-3¢-yl)aminocarboxyquinolines 8-12 have been synthesized in order to determine their antimicrobial activities and feasible structure-activity relationships. The synthesized compounds and reference drugs have been tested in vitro against various strains of bacteria: E. coli ATCC 25922, B. subtilis ATCC 1633 and S. aureus ATCC 25923 and the fungi: C. albicans ATCC 2091, A. niger ATCC 9029 and C. krusei ATCC 6258. Microbiological results showed that the synthesized compounds possessed a broad spectrum of antimicrobial activity against the microorganisms tested. 1-Ethyl-6-fluoro-7-piperazinyl-4-oxo-3-[2¢-(o-methoxyphneyl)-4¢-oxo-1¢,3¢-thiazolidin-3¢-yl)aminocarboxyquinoline 10 has displayed more potent antibacterial activity as compared to standard drug, chloroamphenicol and rest of the compounds of this series. This compound has also exhibited significant antifungal activities, which is not more than that of fluconazole. The structural assignments of newly synthesized compounds are based on IR, 1H NMR, mass spectral studies and elemental analysis