Bacteroides thetaiotaomicron Starch Utilization Promotes Quercetin Degradation and Butyrate Production by Eubacterium ramulus

Consumption of flavonoids has been associated with protection against cardiovascular and neurodegenerative diseases. Most dietary flavonoids are subjected to bacterial transformations in the gut where they are converted into biologically active metabolites that are more bioavailable and have distinct effects relative to the parent compounds. While some of the pathways involved in the breakdown of flavonoids are emerging, little it is known about the impact of carbon source availability and community dynamics on flavonoid metabolism. This is relevant in the gut where there is a fierce competition for nutrients. In this study, we show that metabolism of one of the most commonly consumed flavonoids, quercetin, by the gut-associated bacterium Eubacterium ramulus is dependent on interspecies cross-feeding interactions when starch is the only energy source available. E. ramulus can degrade quercetin in the presence of glucose but is unable to use starch for growth or quercetin degradation. However, the starch-metabolizing bacterium Bacteroides thetaiotaomicron, which does not metabolize quercetin, stimulates degradation of quercetin and butyrate production by E. ramulus via cross-feeding of glucose and maltose molecules released from starch. These results suggest that dietary substrates and interactions between species modulate the degradation of flavonoids and production of butyrate, thus shaping their bioavailability and bioactivity, and likely impacting their health-promoting effects in humans

Isoprene photochemistry over the Amazon rainforest

Isoprene photooxidation is a major driver of atmospheric chemistry over forested regions. Isoprene reacts with hydroxyl radicals (OH) and molecular oxygen to produce isoprene peroxy radicals (ISOPOO). These radicals can react with hydroperoxyl radicals (HO_2) to dominantly produce hydroxyhydroperoxides (ISOPOOH). They can also react with nitric oxide (NO) to largely produce methyl vinyl ketone (MVK) and methacrolein (MACR). Unimolecular isomerization and bimolecular reactions with organic peroxy radicals are also possible. There is uncertainty about the relative importance of each of these pathways in the atmosphere and possible changes because of anthropogenic pollution. Herein, measurements of ISOPOOH and MVK + MACR concentrations are reported over the central region of the Amazon basin during the wet season. The research site, downwind of an urban region, intercepted both background and polluted air masses during the GoAmazon2014/5 Experiment. Under background conditions, the confidence interval for the ratio of the ISOPOOH concentration to that of MVK + MACR spanned 0.4–0.6. This result implies a ratio of the reaction rate of ISOPOO with HO_2 to that with NO of approximately unity. A value of unity is significantly smaller than simulated at present by global chemical transport models for this important, nominally low-NO, forested region of Earth. Under polluted conditions, when the concentrations of reactive nitrogen compounds were high (>1 ppb), ISOPOOH concentrations dropped below the instrumental detection limit (<60 ppt). This abrupt shift in isoprene photooxidation, sparked by human activities, speaks to ongoing and possible future changes in the photochemistry active over the Amazon rainforest

Isoprene photochemistry over the Amazon rainforest

Isoprene photooxidation is a major driver of atmospheric chemistry over forested regions. Isoprene reacts with hydroxyl radicals (OH) and molecular oxygen to produce isoprene peroxy radicals (ISOPOO). These radicals can react with hydroperoxyl radicals (HO2) to dominantly produce hydroxyhydroperoxides (ISOPOOH). They can also react with nitric oxide (NO) to largely produce methyl vinyl ketone (MVK) and methacrolein (MACR). Unimolecular isomerization and bimolecular reactions with organic peroxy radicals are also possible. There is uncertainty about the relative importance of each of these pathways in the atmosphere and possible changes because of anthropogenic pollution. Herein, measurements of ISOPOOH and MVK+MACR concentrations are reported over the central region of the Amazon basin during the wet season. The research site, downwind of an urban region, intercepted both background and polluted air masses during the GoAmazon2014/5 Experiment. Under background conditions, the confidence interval for the ratio of the ISOPOOH concentration to that of MVK+MACR spanned 0.4-0.6. This result implies a ratio of the reaction rate of ISOPOO with HO2 to that with NO of approximately unity. A value of unity is significantly smaller than simulated at present by global chemical transport models for this important, nominally low-NO, forested region of Earth. Under polluted conditions, when the concentrations of reactive nitrogen compounds were high (&gt;1 ppb), ISOPOOH concentrations dropped below the instrumental detection limit (&lt;60 ppt). This abrupt shift in isoprene photooxidation, sparked by human activities, speaks to ongoing and possible future changes in the photochemistry active over the Amazon rainforest

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The genomic basis of parasitism in the Strongyloides clade of nematodes.

Soil-transmitted nematodes, including the Strongyloides genus, cause one of the most prevalent neglected tropical diseases. Here we compare the genomes of four Strongyloides species, including the human pathogen Strongyloides stercoralis, and their close relatives that are facultatively parasitic (Parastrongyloides trichosuri) and free-living (Rhabditophanes sp. KR3021). A significant paralogous expansion of key gene families--families encoding astacin-like and SCP/TAPS proteins--is associated with the evolution of parasitism in this clade. Exploiting the unique Strongyloides life cycle, we compare the transcriptomes of the parasitic and free-living stages and find that these same gene families are upregulated in the parasitic stages, underscoring their role in nematode parasitism

Cranberry (Vaccinium macrocarpon) Juice Precipitate Pigmentation Is Mainly Polymeric Colors and Has Limited Impact on Soluble Anthocyanin Loss

Anthocyanins degrade in fruit juice during storage, reducing juice color quality and depleting the health-promoting components of juice. Common water-soluble products of anthocyanins’ chemical degradation are known, but little is known about the contribution of the insoluble phase to loss processes. Cranberry juice and isolated anthocyanins were incubated at 50 °C for up to 10 days to determine polyphenol profiles and degradation rates. Anthocyanin-proanthocyanidin heteropolymers were analyzed via Matrix Assisted Laser Desorption/Ionization (MALDI)- Time of Flight (TOF) Mass Spectrometry (MS). Formation of soluble protocatechuic acid accounted for 260 ± 10% and insoluble materials for 80 ± 20% of lost soluble cyanidin-glycosides in juice, over-representations plausibly due to quercetin and (epi)catechin in cranberry juice and not observed in the values of 70 ± 20% and 16 ± 6% in the purified anthocyanin system. Loss processes of soluble peonidin-glycosides were better accounted for, where 31 ± 2% were attributable to soluble vanillic acid formation and 3 ± 1% to insoluble materials in cranberry juice and 35 ± 5% to vanillic acid formation and 1.6 ± 0.8% to insoluble materials in the purified anthocyanin system. Free anthocyanins were below quantifiable levels in precipitate, implying most anthocyanins in precipitate were polymeric colors (PCs). PCs in the precipitate included cyanidin- and peonidin-hexosides and -pentosides covalently bonded to procyanidins. Therefore, formation of cranberry juice precipitate does not deplete a large portion of soluble anthocyanins; rather, the precipitate’s pigmentation results from PCs that are also present in the soluble phase

The antisaccade task: visual distractors elicit a location-independent planning \u27cost\u27

The presentation of a remote - but not proximal - distractor concurrent with target onset increases prosaccade reaction times (RT) (i.e., the remote distractor effect: RDE). The competitive integration model asserts that the RDE represents the time required to resolve the conflict for a common saccade threshold between target- and distractor-related saccade generating commands in the superior colliculus. To our knowledge however, no previous research has examined whether remote and proximal distractors differentially influence antisaccade RTs. This represents a notable question because antisaccades require decoupling of the spatial relations between stimulus and response (SR) and therefore provide a basis for determining whether the sensory- and/or motor-related features of a distractor influence response planning. Participants completed pro- and antisaccades in a target-only condition and conditions wherein the target was concurrently presented with a proximal or remote distractor. As expected, prosaccade RTs elicited a reliable RDE. In contrast, antisaccade RTs were increased independent of the distractor\u27s spatial location and the magnitude of the effect was comparable across each distractor location. Thus, distractor-related antisaccade RT costs are not accounted for by a competitive integration between conflicting saccade generating commands. Instead, we propose that a visual distractor increases uncertainty related to the evocation of the response-selection rule necessary for decoupling SR relations