Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12.

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B.

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown.

Substantial differences in soil viral community composition within and among four Northern California habitats.

Viruses contribute to food web dynamics and nutrient cycles in diverse ecosystems, yet the biogeographical patterns that underlie these viral dynamics are poorly understood, particularly in soil. Here, we identified trends in soil viral community composition in relation to habitat, moisture content, and physical distance. We generated 30 soil viromes from four distinct habitats (wetlands, grasslands, woodlands, and chaparral) by selectively capturing virus-sized particles prior to DNA extraction, and we recovered 3432 unique viral 'species' (dsDNA vOTUs).

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development.

Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other.

A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil.

Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following "wet-up", when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up.

Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO-derived C from host to virus via DNA stable-isotope probing and metagenomic analysis.

Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems.

The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are shaped by both current and historical soil environmental conditions. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) with an HO labeling experiment to identify actively growing soil microorganisms and their genomic capacities. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies.

Methane-derived carbon flows into host-virus networks at different trophic levels in soil.

The concentration of atmospheric methane (CH) continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts.

Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater.

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel.

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes.

Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses.

Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities.

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean.

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run.

Mock communities have been used in microbiome method development to help estimate biases introduced in PCR amplification and sequencing and to optimize pipeline outputs. Nevertheless, the strong value of routine mock community analysis beyond initial method development is rarely, if ever, considered. Here we report that our routine use of mock communities as internal standards allowed us to discover highly aberrant and strong biases in the relative proportions of multiple taxa in a single Illumina HiSeqPE250 run.

KINETICS STUDY ON KETOPROFEN RELEASE FROM MINI TABLETS AND MULTI-COMPARTMENT SYSTEMS.

Thanks to multi-compartment systems it is possible to modify drug release. Two types of mini tablets containing 12.5 mg of ketoprofen were made: mini tablets of immediate (IR) and sustained (SR) release.

Influence of CYP2D6 and CYP2C19 genetic polymorphism on the pharmacokinetics of tolperisone in healthy volunteers.

Purpose: This is the first study that connects pharmacokinetics of tolperisone with genetic polymorphism of the enzymes involved in its metabolism in human. We aimed to identify the influence of polymorphism of two main enzymes (CYP2D6 and CYP2C19) on pharmacokinetic profile of parent drug.

Methods: In a single-dose study, 28 healthy Caucasian male volunteers received an oral dose of 150 mg of tolperisone.

Bovine corneal epithelial primary cultures as an in vitro model for ophthalmic drugs studies.

In the recent years a significant development of investigations with regard to bioavailability of ocular drugs has been noticed. The corneal epithelial barrier is the main pathway for ocular penetration of topically applied ophthalmic drugs into the anterior chamber. To work out an in vitro model of bovine corneal epithelial primary cultures and exercise it for permeability research with lipophilic and hydrophilic markers, permeability coefficients estimation of the 6-carboxyfluorescein and rhodamin B was made.

Usefulness of the parent compound determination in bioequivalence evaluation of clopidogrel generic products.

Objective: The aim of the presented comparative study was to evaluate the bioavailability of clopidogrel (CAS 113665-84-2) formulations containing clopidogrel bisulfate (CAS 135046-48-9, CBS) 75 mg based on the parent compound (CBS) and its metabolite SR 26334 - clopidogrel carboxylic acid (CAS 144457-28-3, CCA) determination.

Methods: This paper presents the results of a comparative, randomized, two-way cross-over study on 48 healthy male volunteers assessing the bioequivalence of two products of clopidogrel 75 mg in form of film-coated tablets. In each of the two periods, separated by a 7-day washout period, a single dose of 150 mg (2 x 75 mg) of test and reference preparations was administered under fasting condition.

[The effect of selenium and vitamin E on the healing process of experimental corneal lesions in the eye of the rabbit].

Purpose: Evaluation of antioxidants: selenium and vitamin E efficacy in the treatment of experimental corneal lesion.

Material And Methods: Solution of selenium in 0.9% NaCl, concentration 0.

[Gentamicin kinetics in the blood and aqueous humor of the rabbit eye after intramuscular and subconjunctival administration].

Investigations were performed in rabbits which were given gentamycin intramuscularly and subconjunctivally. After subconjunctival application gentamycin passes quickly into the eye and its therapeutical level persists up to 1 hour. After intramuscular injection gentamycin is passing slower into the aqueous but persists there longer (the therapeutical level--up to 5.

[Bioavailability of drugs applied to the eye externally].

There are following forms of the most frequently used ocular therapeutics: eye drops, ointments and inserts. In dependence on the physico-chemical properties of the therapeutical substance and the kind of disease one has to formulate the form of the drug in the manner to obtain its maximal bioavailability. By increasing their viscosity one can keep the watery solutions in the conjunctival sac for around 60 min.