DCA-treated colon cancer cells exhibited higher ROS generation, membrane blebbing, activation of mitochondrial apoptotic pathway, and formation of apoptotic bodies compared to untreated cells. DCA exposure also resulted in micronuclei formation accompanied by a dose-dependent response in NFκb activation that was attenuated by cotreatment. The above studies clearly demonstrate that hydrophobic BAs induce cellular oxidative stress through elevated reactive oxygen and nitrogen species production with similar results observed between human liver and colon cell lines. Interestingly, human HCC cells treated with hydrophobic primary CDCA also displayed cell cycle arrest, caspase-9-like activity, poly ADP-ribose polymerase cleavage, dose-dependent sites of DNA lesions, and extensive nuclear fragmentation. These cells also showed activation of ERK1/2 leading to the phosphorylation and stabilization of myeloid cell leukemia sequence 1 in a mitogenactivated protein kinase-dependent manner which conferred greater resistance to chemotherapeutic drugs. These findings strongly support that excessive levels of hydrophobic BA can exert a carcinogenic effect on enterohepatic tissues by promoting genomic instability through oxidative injury. Figure 3 provides an overview of the implicated carcinogenic consequences of BA dysregulation, gut dysbiosis, and insulin resistance. Several synthetic drugs such as colesevelam and colestimide, designed to sequester BAs, have demonstrated efficacy in improving insulin resistance and glucose tolerance. BA receptor agonists also appeared to be promising in the management of obesity and diabetes related symptoms. Specifically, synthetic retinoid such as acyclic retinoid was investigated for its beneficial effect on obesity-related liver tumorigenesis, since RXRα, a heterodimer partner of FXR, square plastic plant pot was found to be repressed in early stages of HCC due to phosphorylation by the Ras/MAPK signaling pathway. Results indicate that ACR inhibited the Ras/MAPK pathway, ameliorated liver steatosis, improved insulin sensitivity, and decreased inflammation.

Ultimately, ACR appears promising in restoring RXRα function in the liver, making it an effective chemoprevention drug against HCC progression. With the intestinal microbiota implicated as one of the key players in the progression of liver and colon carcinogenesis in obese and diabetic patients, selective modification of the gut microbial composition has been extensively researched as a viable alternative or additive to current treatment plans. Prebiotics promote the growth of beneficial bacteria while probiotics are live microorganisms, administered exogenously, which provide a benefit beyond nutrition. Most prebiotics exist in the form of non-digestible carbohydrates and exert protective effects against liver and colon cancer. Dietary fibers shortened GI transit time to reduce the length of exposure to toxic metabolites such as hydrophobic BAs and bacterial toxins while aiding in their incorporation in feces for excretion. In addition, these fibers enhanced the growth of beneficial bacteria such as Bifidobacteria, lowered intestinal pH, and inhibited the growth of harmful bacteria. An increase in bifidobacteria is the signature of prebiotic treatment using insulintype fructans or galactooligosaccharides. Other resistant dietary fibers such as pomegranate peel extract and natural phytoalexin resveratrol can alter the gut microbiome in favor of bifidobacteria while lowering inflammatory markers in the colon and visceral adipose tissue. Short chain fatty acids , the fermented end products of dietary fibers, are recognized for their ability to inhibit growth and promote apoptosis in colon and liver cancer cells. SCFAs can also activate various drug metabolizing enzymes to decrease DNA mutation and reduce cancer risk. Complementing SCFAs with fish oil selectively reduced unsaturated fatty acid accumulation in the liver, improving hepatic fat oxidation and inflammation. Furthermore, probiotics have been suggested as a tool to manage inflammatory bowel disease. Although no general consensus exists for the beneficial effects of probiotics in obese, diabetic, and NAFLD patients, reduced hepatic total fatty acid content and serum alanine aminotransferase levels were noted in rodent models treated with probiotics.

A synergistic effect of probiotics and blueberry husks in preventing colon carcinomas and subsequent liver tumors has been observed in rats. Blueberry husks alone significantly decrease the number of colonic ulcers and dysplastic lesions while probiotics alone improved liver function by decreasing parenchymal infiltration and bacterial translocation. Thus, the combination treatment of probiotics and blueberry husks delayed colonic carcinogenesis and prevented hepatic injuries. The combined treatment also reduced endotoxin-producing enterobacteriaceae and increased beneficial, anti-inflammatory lactobacilli. Synbiotics, mixtures of probiotics and prebiotics, were noted to lower colon cancer risk through improved insulin resistance, reduced inflammation, and preservation of gut barrier integrity in rats fed a high-fat diet. In terms of gut microbial ecology, synbiotic treatment significantly increased fecal Lactobacillus species at the expense of potentially pathogenic E. coli and Staphylococcus, thus lowering the endotoxin level in cirrhotic patients. Simple dietary changes can also aid in reversing BA dysregulation and intestinal microbiome derangement. Vitamin B6 can improve colon health by significantly reducing hydrophobic LCA levels in the colon, creating a reduced LCA to DCA ratio. LCA was 20- fold more toxic than DCA toward liver and colon cancer cells, and vitamin B6 helped with detoxifying enzymes and decreased DNA damage.170 Moreover, various naturally derived products are also under investigation including the antioxidant tempol which reduced obesity and improved insulin resistance in mice fed a high-fat diet by activating bile salt hydrolase to increase intestinal tauro-beta-muricholic acid, an FXR antagonist. Tempol appears to exert its antiobesity effects through FXR since inhibition of intestinal FXR promoted diet-induced obesity and insulin resistance. Tempol was also able to shift the gut microbial profile from firmicutes toward bacteroidetes dominance. Plant-based products such as burdock powder and genistein also showed moderate efficacy in normalizing BA homeostasis and the gut microbiome in animal models. The proposed beneficial effects on BA dysregulation and gut dysbiosis by pharmacological and dietary intervention are described in Figure 4. In this genome release, we report on the first assembled genome of a member of the genus Arctostaphylos. 

Our genome assembly is part of the California Conservation Genomics Project , the goal of which is to establish patterns of genomic diversity across the state of California and its many habitats. The CCGP will sequence the complete genomes of approximately 150 carefully selected species projects. Many of these taxa are threatened or endangered, and therefore in need of conservation management in the face of rapidly accelerating biodiversity decline. The combined reference genome plus landscape genomics approach of the CCGP, based on the resequencing of many individuals of each target species across the state, will allow the identification of hotspots of diversity across California and provide a framework for informed conservation decisions and management plans. Manzanitas are among the most conspicuous and dominant native chaparral species in the California Floristic Province , a biodiversity hotspot characterized by a Mediterranean-type climate with hot, dry summers and cool, wet winters. These plants comprise the most diverse woody genus in the CFP , and their diversity has long fascinated taxonomists. Manzanitas serve essential roles in their native ecosystems, including rapidly regenerating in fired-disturbed areas, and providing food resources for pollinators and fruit-eating animals . In addition, these plants are of great importance for conservation management: over half of the more than 100 morphologically defined manzanita species and subspecies are narrow endemics with highly restricted distributions and are considered rare and/or endangered . In contrast to their importance in ecology, evolution, and conservation studies, genomic resources for manzanitas are nearly nonexistent beyond investigations into karyotypes of diploid and tetraploid species . In this study, we present the first genome sequence of a manzanita. Big berry manzanita, Arctostaphylos glauca , is a widespread diploid species common in northern Baja California and across southern and coastal central California that is hypothesized to be the progenitor of several potential hybrid manzanita species . With funding and support from the CCGP, 25 liter square pot we created this scaffold-level assembly using a hybrid de novo assembly approach that combines Hi-C chromatin-proximity and PacBio HiFi long-read sequencing data. This genome assembly will provide a robust basis for studying the diversification and evolutionary history of Arctostaphylos in the CFP.A Dovetail Hi-C library was prepared in a similar manner as previously described . For each library, chromatin was fixed in place with formaldehyde in the nucleus. Extracted, fixed chromatin was digested with DpnII, the 5′ overhangs were filled in with biotinylated nucleotides, and free blunt ends were ligated. After ligation, crosslinks were reversed, and the DNA purified from protein. Purified DNA was treated to remove biotin that was not internal to ligated fragments. The DNA was then sheared to ~350 bp mean fragment size and sequencing libraries were generated using NEBNext Ultra enzymes and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of each library. The libraries were prepared and sequenced on an Illumina HiSeq X by Dovetail Genomics .The CCGP assembly protocol version 1.0 uses PacBio HiFi reads and Hi-C chromatin capture data for the generation of high-quality and highly contiguous nuclear genome assemblies. The output corresponding to a diploid assembly consists of two pseudo haplotypes .

The alternate consists of haplotigs in heterozygous regions and is not as complete and more fragmented. Given the characteristics of the latter, it cannot be considered on its own but as a complement of the primary assembly . Arctostaphylos is the third genus with a genome assembly in the heath family, Ericaceae, following release of assembled genome sequences of Rhododendron and Vaccinium . These two genera are of significant economic importance: many species, hybrids, and cultivars of Rhododendron, including rhododendron and azalea, are important landscape and ornamental plants, and the fruits of many Vaccinium species, which include cranberry, blueberry, and huckleberry, are consumed by humans and other animals. Species in the Ericaceae are also notable for their ability to tolerate acidic and nutrient-poor soils that often characterize boreal forests and bogs, allowing them to thrive in habitats that are inaccessible to most species. Their tolerance for these conditions is due in part to the formation of mutualistic associations between the roots of the plants and soil fungi of a type unique to the heath family known as ericoid mycorrhizae. Ericoid mycorrhizae are distinct from common mycorrhizal associations found in most angiosperms, and are far less well understood . Complete genome sequences from three genera in this family will provide a strong foundation for investigating the basis of this unique mutualism and its ability to promote survival in inhospitable soils. The size of the A. glauca assembly is 547Mb, which is similar to the two Rhododendron genomes and half that of V corymbosum, which is tetraploid . The tetraploid nature of V. corymbosum also explains the vastly greater number of duplicated genes in its assembly compared to the two diploid assemblies. The scaffold N50 of the A. glauca assembly is longer than R. williamsianum, and close to R. simsii and V. corymbosum, suggesting that the contiguity of Arctostaphylos is comparable to the other taxa . Analysis using Repeat Modeler indicated that 57.71% of the A. glauca genome is composed of different categories of repetitive elements . In contrast, analysis using RepeatModeler identified only 26%, 47.5%, and 44.3% of the genome comprising repeat elements in R. williamsianum, R. simsii, and V. corymbosum respectively. The BUSCO completeness assessment of the A. glauca assembly is higher than R. williamsianum and close to the V. corymbosum , indicating that our final assembly is high quality . Overall, the A. glauca, R. simsii and V. corymbosum genomes are of comparably high contiguity and completeness. The lower contiguity and completeness of the R. williamsianum genome may be due to the lack of HiFi or other longread data in the assembly. This explanation is consistent with other studies demonstrating improved assembly with the inclusion of longer reads . Although the big berry manzanita is a common and widespread species, nearly half of the 60+ manzanita species are rare or threatened. Many are now represented by only one or two populations, and are thus vulnerable to complete eradication by the increasingly common and intense wildfires experienced across California each year. Our manzanita genome sequence will help fulfill the overall goal of the CCGP, serving as a key resource to assess genetic diversity in these threatened endemics and move forward with coordinated conservation programs.Sangiovese is the most important Italian red grape variety, with origins in Tuscany and Calabria in the south of Italy. Through time, Sangiovese has always been considered as a good-quality cultivar for wine production. Today, it is the basis of internationally known DOC and DOCG wines from Tuscany in Italy, the region where it is most cultivated. Sangiovese is also grown in Argentina, California, France, and in other countries such Australia and Chile, but to a lesser extent.