Small molecules, big targets: drug discovery faces the protein-protein interaction challenge.

Protein-protein interactions (PPIs) are of pivotal importance in the regulation of biological systems and are consequently implicated in the development of disease states. Recent work has begun to show that, with the right tools, certain classes of PPI can yield to the efforts of medicinal chemists to develop inhibitors, and the first PPI inhibitors have reached clinical development. In this Review, we describe the research leading to these breakthroughs and highlight the existence of groups of structurally related PPIs within the PPI target class. For each of these groups, we use examples of successful discovery efforts to illustrate the research strategies that have proved most useful.JS, DES and ARB thank the Wellcome Trust for funding.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nrd.2016.2

The Association between Intrauterine Inflammation and Spontaneous Vaginal Delivery at Term: A Cross-Sectional Study

BACKGROUND:Different factors contribute to the onset of labor at term. In animal models onset of labor is characterized by an inflammatory response. The role of intrauterine inflammation, although implicated in preterm birth, is not yet established in human term labor. We hypothesized that intrauterine inflammation at term is associated with spontaneous onset of labor. METHODS/RESULTS:In two large urban hospitals in the Netherlands, a cross-sectional study of spontaneous onset term vaginal deliveries and elective caesarean sections (CS), without signs of labor, was carried out. Placentas and amniotic fluid samples were collected during labor and/or at delivery. Histological signs of placenta inflammation were determined. Amniotic fluid proinflammatory cytokine concentrations were measured using ELISA. A total of 375 women were included. In term vaginal deliveries, more signs of intrauterine inflammation were found than in elective CS: the prevalence of chorioamnionitis was higher (18 vs 4%, p = 0.02) and amniotic fluid concentration of IL-6 was higher (3.1 vs 0.37 ng/mL, p<0.001). Similar results were obtained for IL-8 (10.93 vs 0.96 ng/mL, p<0.001) and percentage of detectable TNF-alpha (50 vs 4%, p<0.001). CONCLUSIONS:This large cross-sectional study shows that spontaneous term delivery is characterized by histopathological signs of placenta inflammation and increased amniotic fluid proinflammatory cytokines

Bradyrhizobium elkanii nod regulon: insights through genomic analysis

Abstract A successful symbiotic relationship between soybean [Glycine max (L.) Merr.] and Bradyrhizobium species requires expression of the bacterial structural nod genes that encode for the synthesis of lipochitooligosaccharide nodulation signal molecules, known as Nod factors (NFs). Bradyrhizobium diazoefficiens USDA 110 possesses a wide nodulation gene repertoire that allows NF assembly and modification, with transcription of the nodYABCSUIJnolMNOnodZ operon depending upon specific activators, i.e., products of regulatory nod genes that are responsive to signaling molecules such as flavonoid compounds exuded by host plant roots. Central to this regulatory circuit of nod gene expression are NodD proteins, members of the LysR-type regulator family. In this study, publicly available Bradyrhizobium elkanii sequenced genomes were compared with the closely related B. diazoefficiens USDA 110 reference genome to determine the similarities between those genomes, especially with regards to the nod operon and nod regulon. Bioinformatics analyses revealed a correlation between functional mechanisms and key elements that play an essential role in the regulation of nod gene expression. These analyses also revealed new genomic features that had not been clearly explored before, some of which were unique for some B. elkanii genomes

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

<p>Abstract</p> <p>Background</p> <p><it>Sinorhizobium meliloti </it>is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the <it>Medicago sativa </it>plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of <it>S. meliloti </it>strains AK83 and BL225C, we sequenced the complete genomes for these two strains.</p> <p>Results</p> <p>With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.</p> <p>Conclusions</p> <p>In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.</p

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions

Nitrification gene ratio and free ammonia explain nitrite and nitrous oxide production in urea-amended soils

The atmospheric concentration of nitrous oxide (N₂O), a potent greenhouse gas and ozone-depleting chemical, continues to increase, due largely to the application of nitrogen (N) fertilizers. While nitrite (NO₂⁻) is a central regulator of N₂O production in soil, NO₂⁻ and N₂O responses to fertilizer addition rates cannot be readily predicted. Our objective was to determine if quantification of multiple chemical variables and structural genes associated with ammonia (NH₃)- (AOB, encoded by amoA) and NO₂⁻ -oxidizing bacteria (NOB, encoded by nxrA and nxrB) could explain the contrasting responses of eight agricultural soils to five rates of urea addition in aerobic microcosms. Significant differences in NO₂⁻ accumulation and N₂O production by soil type could not be explained by initial soil properties. Biologically-coherent statistical models, however, accounted for 70–89% of the total variance in NO₂⁻ and N₂O. Free NH₃ concentration accounted for 50–85% of the variance in NO₂⁻ which, in turn, explained 62–82% of the variance in N₂O. By itself, the time-integrated nxrA:amoA gene ratio explained 78 and 79% of the variance in cumulative NO₂⁻ and N₂O, respectively. In all soils, nxrA abundances declined above critical urea addition rates, indicating a consistent pattern of suppression of Nitrobacter-associated NOB due to NH₃ toxicity. In contrast, Nitrospira-associated nxrB abundances exhibited a broader range of responses, and showed that long-term management practices (e.g., tillage) can induce a shift in dominant NOB populations which subsequently impacts NO₂⁻ accumulation and N₂O production. These results highlight the challenges of predicting NO₂⁻ and N₂O responses based solely on static soil properties, and suggest that models that account for dynamic processes following N addition are ultimately needed. The relationships found here provide a basis for incorporating the relevant biological and chemical processes into N cycling and N₂O emissions models

A pilot study of fecal bile acid and microbiota profiles in inflammatory bowel disease and primary sclerosing cholangitis

Byron P Vaughn,1 Thomas Kaiser,2,3 Christopher Staley,2,3 Matthew J Hamilton,2 Jon Reich,1 Carolyn Graiziger,1 Stephanie Singroy,2 Amanda J Kabage,1 Michael J Sadowsky,2,4,5 Alexander Khoruts1,2 1Inflammatory Bowel Program, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota, Minneapolis, MN, USA; 2BioTechnology Institute, University of Minnesota, St Paul, MN, USA; 3Department of Surgery, University of Minnesota, Minneapolis, MN, USA; 4Department of Soil, Water, and Climate, University of Minnesota, St Paul, MN, USA; 5Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA Introduction: Inflammatory bowel disease (IBD) is thought to arise from an abnormal immune response to the gut microbiota. IBD is associated with altered intestinal microbial community structure and functionality, which may contribute to inflammation and complications such as colon cancer and liver disease. Primary sclerosing cholangitis (PSC) is associated with IBD and markedly increases the risk of colon cancer. We hypothesized that secondary bile acids, which are products of microbial metabolism, are increased in PSC patients.Aim: Here, we profiled the fecal bile acid composition and gut microbiota of participants with IBD and PSC, as well as healthy participants. Additionally, we tested the effects of vancomycin, a proposed treatment for PSC, on gut microbiota and fecal bile acid composition in participants with IBD and PSC.Methods: Fecal samples were collected from patients with IBD, IBD/PSC and healthy controls and fecal bile acids and DNA for microbiota analysis were extracted. Fecal bile acids were averaged over a seven-day period. For subjects with IBD/PSC, oral vancomycin 500mg twice a day was administered and fecal samples were collected for up to eleven weeks.Results: Participants with IBD and PSC had less fecal microbial diversity at baseline relative to controls. While there was some evidence of altered conversion of cholic acid to deoxycholic acid, no substantial differences were found in the fecal bile acid profiles of patients with IBD and PSC (n=7) compared to IBD alone (n=8) or healthy controls (n=8). Oral vancomycin was a potent inhibitor of secondary bile acid production in participants with IBD and PSC, particularly deoxycholic acid, although no changes in liver biochemistry patterns were noted over a two week period.Conclusion: In this pilot study, bile acid profiles were overall similar among patients with IBD and PSC, IBD alone, and healthy controls. Microbiota diversity was reduced in those with PSC and IBD compared to IBD alone or healthy controls. Keywords: vancomycin, Crohn&rsquo;s disease, ulcerative coliti

Temperature alters dicyandiamide (DCD) efficacy for multiple reactive nitrogen species in urea-amended soils: Experiments and modeling

Dicyandiamide (DCD) is a nitrification inhibitor (NI) used to reduce reactive nitrogen (N) losses from soils. While commonly used, its effectiveness varies widely. Few studies have measured DCD and temperature effects on a complete set of soil N variables, including nitrite (NO₂¯) measured separately from nitrate (NO₃‾). Here the DCD reduction efficiencies (RE) for nine N availability metrics were quantified in two soils (a loam and silt loam) using aerobic laboratory microcosms at 5–30 °C. Both regression analysis and process modeling were used to characterize the responses. Four metrics accounted for NO₃‾ production and included total mobilized N, net nitrification, maximum nitrification rate, and cumulative NO₃‾ (cNO₃‾). The REs for these NO₃‾ -associated production variables decreased linearly with temperature, and in all cases were below 60% at temperatures ≥22 °C, except for cNO₃‾ in one soil. In contrast, REs for NO₂‾ and nitric oxide (NO) gas production were less sensitive to temperature, ranging from 80 to 99% at 22 °C and 50–95% at 30 °C. Addition of DCD suppressed nitrous oxide (N₂O) production in both soils by 20–80%, but increased ammonia volatilization by 36–210%. The time at which the maximum reduction efficiency occurred decreased exponentially with increasing temperature for most variables. The two-step nitrification process model (2SN) was modified to include competitive inhibition coupled to first-order DCD decomposition. Model versus data comparisons suggested that DCD had indirect effects on NO₂‾ kinetics that contributed to the greater suppression of NO₂‾ and NO relative to NO₃‾. This study also points to the need for NIs that are more stable under increased temperature. The methods used here could help to assess the efficacy and temperature sensitivity of other NIs as well as new microbial inhibitors that may be develope