Reverse pharmacokinetics can be used to guide potential target tissues/organs/molecules, and then further physiologically relevant pharmacological models are designed to discover bio-active compounds and reveal their corresponding mechanisms. It is worth noting that many compounds show low solubility, which limits their clinical efficiency and restricts their clinical use. Fortunately, there are multiple ways to enhance the bio-availability, such as cocrystallization and the formation of phospholipid complexes and nanoemulsions.Finally, based on the hypothesis that drugs targeting EMT have both antifibrotic and anticancer effects, many important mediators contributing to EMT have been discovered. Additionally, a great number of compounds suppress EMT in tumor and fibrosis by targeting these mediators. It is hoped that many new drugs are designed and developed in the future based on the aforementioned mediators to treat tumors and fibrosis.The first step in the aerobic nitrification process is the oxidation of ammonia to nitrite, mediated mainly by AOB or AOA in soil environments. The most numerous AOB isolated or detected by non-cultural methods in aerobic agricultural surface soils are consistently members of the Nitrosospira genus. Nitrosospira briensis C-128 is a chemolithoautotrophic ammoniaoxidizing betaproteobacterium isolated from a fertilized soil under cultivation for blueberry in Falmouth, Massachusetts, USA in 1971. The genome of Nitrosospira briensis C-128 is the third genome sequence from the genus Nitrosospira to be published and thus provides an important comparison among Nitrosospira. This report includes a summary of the genome sequence and selected features for Nitrosospira briensis C-128 and results are publically available in GenBank accession CP012371.Nitrosospira briensis was described by Winogradsky and & Winogradsky in 1933 as an ammonia-oxidizing bacterium isolated from soil.

The genus name, Nitrosospira, is derived from two Latin roots: nitrosus, meaning nitrous, and spira, indicating spiral. The species name briensis,black plastic plant pots refers to the original isolation location near Brie, France. The culture described by Winogradsky & Winogradsky was not maintained and reisolation of a replacement strain was reported by Watson in 1971. At approximately the same time, N. briensis strainC-128 was isolated by enrichment culturing from a surface soil sample collected from a fertilized blueberry patch in East Falmouth, Massachusetts in 1971 . In 1993, the genus Nitrosospira was emended to include the former genera of Nitrosovibrio and Nitrosolobus based on the high identities of the 16S rRNA gene sequences. Nitrosospira briensis was designated the type species for the genus with strain C- 76 as the type strain . The full-length 16S rRNA gene sequence of N. briensis C-128 is 99 % identical to the N. briensis strain C-76/ Nsp10 sequence . The culture of N. briensis strain C-128 was received in the Norton laboratory from F. Valois in 1995. Nitrosospira briensis C-128 is presently maintained in a culture collection at WHOI and may be obtained upon request from J.M. Norton. Classification and general features of Nitrosospira briensis C-128 are provided as Minimum Information about the Genome Sequence in Table 1. Electron micrographs of the pure culture organism are shown in Fig. 2 revealing the tight spirals visible with TEM negative staining and the convoluted surface of this Nitrosospira as revealed by SEM.Nitrosospira briensis C-128 was chosen for sequencing through the Community Science Program of the DOE Joint Genome Institute as an important representative of the AOB to improve the scope and quality of intra- and inter-generic comparisons in the Nitrosomonadales. The chemolithotrophic metabolism of the AOB, the pathways for production of nitrous oxide and urea metabolism were additional motivating interests in sequencing this genome. Sequencing, finishing, and annotation were accomplished by JGI. The genome sequence has been deposited in the Genome OnLine Database and is part of the NCBI Reference Sequence Collection.

A summary of the project information is found in Table 2.The genomic DNA of Nitrosospira briensis C-128 was sequenced at the DOE JGI using the Pacific Biosciences sequencing technology. All general aspects of sample handling, library construction and sequencing followed JGI isolate sequencing protocols. A PacBio SMRTbell™ library was constructed and sequenced on the PacBio RS platform, which generated 148,206 reads totaling 519.8Mbp. Raw reads were assembled using HGAP v. 2.2.0.p1 . The final draft assembly contained one contig in one scaffold, totaling 3.2 Mbp in size. The input read coverage was 176.1×. An earlier version of the genome was sequenced using the Illumina Hi-Seq 2000 platform. However, this earlier sequence assembly JHVX00000000.1 remained in 31 scaffolds with the nearly identical repeats of several key catabolic gene clusters remaining unresolved. Previously, genome closure for Nitrosospira was achieved only after extensive directed finishing to correctly assemble long nearly identical repeats of gene clusters encoding key catabolic modules including ammonia monooxygenase for the activation of substrate and hydroxylamine dehydrogense and hemecytochrome c proteins for the extraction of electrons and their delivery to the quinone pool in the membrane. The long read capability of the PacBio platform and our depth of coverage enabled sufficient discrimination of repeats to assemble across multiple nearly identical regions into a single contig representing the chromosome of the bacterium. For predicted genes outside of gaps and repeat regions the PacBio and the Illumina predicted genes were 100 % identical. Therefore, we did not combine the Illumina Hi-Seq data with the PacBio data for the complete genome sequence CP012371 reported here.Genes were identified using Prodigal , as part of the JGI’s Microbial annotation pipeline followed by a round of manual curation using GenePRIMP. The predicted CDSs were translated and used to search the NCBI nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. Transfer RNA genes were identified using the tRNAScanSE tool. Other non-coding RNAs were found using INFERNA. Further gene prediction and manual curation was performed within the Integrated Microbial Genomes platform developed at JGI.The genome of Nitrosospira briensis C-128 contains 3,210,113-bp in one chromosome with a GC content of 53.25 % and no plasmids .

The genome contains one complete ribosomal RNA operon similar to other AOB. Coding bases comprised 85.93 % of the total. We identified 3018 protein encoding genes, 55 RNA genes and 130 pseudogenes. For the identified genes, 74.23 % had a function prediction associated with them. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 % confirming species delineation. The genome statistics are summarized in Table 3 and genes associated with COG functional categories are summarized in Table 4.Alcohol consumption has been associated with an increased risk of developing colorectal cancer . One large meta-analysis reported an increased relative risk of 1.1 for developing CRC when consuming more than 2 alcoholic beverages per day . Other studies, including a large pooled analysis and meta-analysis , have shown a similar modest risk of developing CRC associated with alcohol consumption at approximately 2 drinks per day and higher risk associated with higher quantities of alcohol consumption. The specific type of alcoholic beverage consumed in the aforementioned studies was not associated with CRC risk. Total alcohol consumption has been shown to increase the risk of developing CRC in familial cases through an interaction with family history by several investigators, but the effects of wine have not been assessed . Controversy over this issue remains, as it has been reported that the risk of developing CRC may depend on the type of alcoholic beverage consumed. Beer intake has been shown to have a strong association with CRC in several studies . Interestingly, in a large population-based cohort study analyzing 28,000 individuals, alcohol intake was associated with an increased risk of rectal cancer; however, this risk was diminished in alcohol drinkers who consumed at least some wine versus those who did not drink any wine at all . In the same study,black plastic planting pots wine intake was associated with a non-significant trend toward decreased risk of developing colon cancer . Moderate wine consumption has been associated with decreased risk of total mortality, an effect attributed to decreased risk of death from cardiovascular causes and protection from cancer and other causes . Light to moderate wine drinkers have been observed to have a lower risk for death from cancer than those who did not drink wine— an effect not observed for consumers of beer and spirits . In a large U.S. mortality study, alcohol was noted to have a trend toward decreased CRC-specific mortality among women —particularly at light consumption levels . Familial CRC is characterized by multi-factorial inherited susceptibility to CRC and represents approximately 20% of CRC cases; another approximately 79% are considered to be sporadic cases. Based on evidence that there is a decreased risk of developing CRC for wine drinkers, that a decreased cancer-related mortality is associated with wine consumption, and that light to moderate alcohol use among female CRC cases results in a trend toward decreased mortality, we set out to determine if wine consumption was associated with favorable effects on tumor characteristics or survival among CRC cases.Using data from the University of California Irvine CRC gene-environment study , incident cases of invasive colorectal carcinoma during the period 1994–1996 were analyzed. Family history of cancer was ascertained via telephone interview.

Familial CRC cases were identified as those having at least 1 first-degree relative with CRC. Amsterdam criteria were used to define hereditary non-polyposis colon cancer families . HNPCC cases and 1 case with clinically diagnosed Familial Adenomatous Polyposis were excluded from the analysis . The remaining sporadic and familial CRC cases were included for analysis by wine consumption frequency group. Food consumption was self-reported via a validated 100-item National Cancer Institute -Block food-frequency questionnaire in which cases were asked to report their usual eating habits during the 1 yr prior to diagnosis of CRC . Frequency of wine , beer , and liquor consumption was recorded, and available responses ranged from “never” to “6+” servings a day. Total daily energy intake, total daily fiber intake, total daily dietary calcium intake, vegetable and fruit consumption, and body mass index were analyzed from FFQ data using the NCI-Block Analysis Program , version 4.0, as previously reported . All cases were dichotomized as either infrequent wine consumers or regular wine consumers . In the same manner, cases were classified as regular or infrequent consumers of beer and liquor. Clinical and demographic data from consented cases were obtained from the Cancer Surveillance Programs of Orange County, Imperial County, and San Diego County, California as described previously . Recorded data included demographic information , histology, tumor grade, stage at presentation, and survival status. Therapeutic information related to the first course of treatment was obtained including surgical treatment rendered at the primary site, treatment with radiation therapy, and use of chemotherapy. Data were abstracted from medical and laboratory records by trained tumor registrars according to Cancer Reporting in California: Vol. 1. Abstracting and Coding Procedures for Hospitals . Tumor site and histology were coded according to criteria specified by the World Health Organization in International Classification of Diseases for Oncology . Primary site code was searched as described previously using the Surveillance, Epidemiology, and End Results site code for colon and rectum . Appendiceal cancers were excluded. Histology codes included adenocarcinoma , mucinous adenocarcinoma , carcinoma , and not otherwise specified . Only invasive cases of cancer were included in the analysis. Staging was grouped into 3 broad categories that could be classified from clinical and pathologic records and defined according to SEER summary staging as localized disease, regional disease, and remote disease . Socioeconomic status quintiles were obtained from the SES variable available in the California Cancer Registry as described previously . This index variable utilized for SES includes a combination of 7 indicator variables for census block data including assessments of educational status, income, and housing information .In this observational study, earlier stage at presentation and improved OS were noted for familial CRC cases who were regular wine consumers prior to the time of diagnosis compared to those that were infrequent wine users. The observed survival benefit persisted after adjustment for age, gender, stage at presentation, SES, BMI, treatment status, and consumption of beer and liquor. In contrast, among sporadic CRC cases, no differences in stage at presentation or survival were noted for regular versus infrequent wine consumers. The observed survival differences based on reported wine consumption were not detected for beer or liquor consumption. Greater than 1/2 of the regular wine consumers in this study were moderate wine consumers .