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The breeding of raspberries (Rubus idaeus L.) and blackberries (R. fruticosus Agg.) has shifted in focus toward traits associated with the sensory qualities and potential health benefits of the fruit, and Rubus wild species have attracted a great deal of attention as new sources of genetic diversity. In this study, the anthocyanin and polyphenol contents and compositions, and three types of antioxidant capacities were compared in mature fruits including raspberries, blackberries, and Japanese wild Rubus species. ‘Blackcap’ black raspberry showed the significantly highest values of total anthocyanin content and total polyphenol content among 12 Rubus species or cultivars. Cyanidin-3-xylosyl-rutinoside was contained only in black raspberries, and was characteristic anthocyanin in Rubus species. R. croceacanthus H. Lev., a Japanese wild species that is adapted to warm regions, had a deep red fruit color, and had the highest total anthocyanin and total polyphenol contents among the four Japanese wild species examined. As for the antioxidant capacities, the highest values were observed in ‘Blackcap’ among 12 Rubus species. Furthermore, a high positive correlation was shown between total anthocyanin or total polyphenol content and antioxidant capacities. In particular, black raspberries and blackberries contained high concentrations of rutin. Thus, rutin might contribute to the high antioxidant capacities in these cultivars.

Black raspberries (BRB) have been shown to inhibit carcinogenesis in a number of systems, with most studies focusing on progression. Previously we reported that an anthocyanin-enriched black raspberry extract (BE) enhanced repair of dibenzo-[a,l]-pyrene dihydrodiol (DBP-diol)-induced DNA adducts and inhibited DBP-diol and DBP-diolepoxide (DBPDE)-induced mutagenesis in a lacI rat oral fibroblast cell line, suggesting a role for BRB in the inhibition of initiation of carcinogenesis. Here we extend this work to protection by BE against DNA adduct formation induced by dibenzo-[a,l]-pyrene (DBP) in a human oral leukoplakia cell line (MSK) and to a second carcinogen, UV light. Treatment of MSK cells with DBP and DBPDE led to a dose-dependent increase in DBP-DNA adducts. Treatment of MSK cells with BE after addition of DBP reduced levels of adducts relative to cells treated with DBP alone, and treatment of rat oral fibroblasts with BE after addition of DBPDE inhibited mutagenesis. These observations showed that BE affected repair of DNA adducts and not metabolism of DBP. As a proof of principle we also tested aglycones of two anthocyanins commonly found in berries, delphinidin chloride and pelargonidin chloride. Delphinidin chloride reduced DBP-DNA adduct levels in MSK cells, while PGA did not. These results suggested that certain anthocyanins can enhance repair of bulky DNA adducts. As DBP and its metabolites induced formation of bulky DNA adducts, we investigated the effects of BE on genotoxic effects of a second carcinogen that induces bulky DNA damage, UV light. UV irradiation produced a dose-dependent increase in cyclobutanepyrimidine dimer levels in MSK cells, and post-UV treatment with BE resulted in lower cyclobutanepyrimidine dimer levels. Post-UV treatment of the rat lacI cells with BE reduced UV-induced mutagenesis. Taken together, the results demonstrate that BE extract reduces bulky DNA damage and mutagenesis and support a role for BRB in the inhibition of initiation of carcinogenesis.

Black raspberries are widely consumed in diets because of their potential health benefits attributed to abundant phytochemicals with biological properties. Twenty polyphenolic profiles (5 anthocyanins and 15 phenolics) were identified by HPLC-MS/MS. 10 compounds (3 anthocyanins and 7 phenolics) were isolated and confirmed by NMR, and two were isolated from Rubus for the first time. Freeze-dried black raspberry powder extracts were purified by polyamide resin with different concentrations of ethanol elution. The 30%, 50%, and 70% fractions exhibited the highest total monomeric anthocyanin, phenolic and flavonoid content, respectively. Moreover, the 30% fraction and compound 8, 9, 11, 17 exhibited optimal antioxidant activity. In α -glycosidase assay, the 70% fraction and compound 16, 17 demonstrated the greatest inhibitory effect. In PTP1B assay, the 30% fraction and compound 9, 11, 16, 17 exhibited the highest inhibitory effect.

Robus coreanus Miquel is widely used in the production of Korean black raspberry (KBR) wine owing to its health benefits and commercial value. The effects of three different commercially available glycosidase enzymes on the volatile compounds in KBR wines were investigated with large-scale fermentation to develop a high-flavour-quality wine. Volatile aroma compounds from the wines were analysed using headspace-solid phase micro-extraction-gas chromatography–mass spectrometry (HS-SPME-GC–MS) and sensory evaluations were performed to evaluate the flavour characteristics. KBR wines treated with commercial enzymes yielded high concentrations of terpenes and esters compared with the control wine because the odourless non-volatile glycosides in KBR wines were converted to their corresponding free forms by the enzymes. HS-SPME-GC–MS-SIM analysis showed that the primary monoterpene compounds in KBR wines treated by the enzymes were myrtenol, linalool, citronellol and a significant quantity of compounds such as 2-phenyl ethanol and ethyl benzoate, which contributed to the flavour of KBR wine, as determined by GC-FID. KBR wines treated with the enzymes exhibited different sensory characteristics from the control wine owing to higher intensity of floral and fruity aromas. KBR wine treated with CYTOLASE PCL5 on a large scale exhibited the highest sensory preference. Copyright © 2017 The Institute of Brewing & Distilling

Alcoholic fermentation (AF) and malolactic fermentation (MLF) both have significant influence on the production of black raspberry wine. In this study, three microbes associated with AF and MLF including S. cerevisiae, T. delbrueckii and O. oeni were used to investigate their combined effect on basic compositional, volatile and sensory property of black raspberry wine, and four fermentation trials including single S. cerevisiae inoculation plus spontaneous MLF (BSU) and controlled MLF with O. oeni (BSO), sequential culture of T. delbrueckii and S. cerevisiae plus spontaneous MLF (BTSU) and controlled MLF (BTSO) were tested and compared. Fermentation results showed MLF in BSU, BSO and BTSO were successful, with respective period of 40, 25 and 23 days, whereas a stuck MLF occurred in BTSU. Volatile compounds were determined by HS-GC-IMS method, with a total of 45 aromas identified. BTSO was distinguished by a significant higher signal intensity of many fruity esters and a lower production of several alcohols and terpenes, which was in agreement with its perception result of strong 'fruity' and slight note of 'solvent' and 'herbaceous' during quantitative descriptive analysis. On the contrary, BSU was found to reinforce the synthesis of most detected volatiles, resulting in the enhancement of both beneficial and off-flavour compounds, therefore scoring lower in the 'global aroma' descriptor. Principal component analysis showed BSU and BSO were similar in the volatile composition, whereas BTSO was quite different. Overall, BTSO had greater potential to be used in the production of black raspberry wine.

We previously reported that the environmental pollutant and tobacco smoke constituent dibenzo[def,p]chrysene (DBP) induced DNA damage, altered DNA methylation and induced oral squamous cell carcinoma (OSCC) in mice. In the present study, we showed that 5% dietary black raspberry (BRB) significantly reduced (P < 0.05) the levels of DBP-DNA adducts in the mouse oral cavity with comparable effect to those of its constitutes. Thus, only BRB was selected to examine if aberrant DNA methylation induced by DBP can be altered by BRB. Using comparative genome-wide DNA methylation analysis, we identified 479 hypermethylated and 481 hypomethylated sites (q < 0.01, methylation difference >25%) between the oral tissues of mice treated with DBP and fed control diet or diet containing BRB. Among the 30 differential methylated sites (DMS) induced by DBP, we found DMS mapped to Fgf3, Qrich2, Rmdn2, and Cbarp were hypermethylated by BRB whereas hypomethylated by DBP at either the exact position or proximal sites; DMS mapped to Vamp3, Ppp1rB1, Pkm, and Zfp316 were hypomethylated by BRB but hypermethylated by DBP at proximal sites. In addition to Fgf3, 2 DMS mapped to Fgf4 and Fgf13 were hypermethylated by BRB; these fibroblast growth factors are involved in regulation of the epithelial–mesenchymal transition (EMT) pathway as identified by IPA. Moreover, BRB significantly reduced (P < 0.05) the tumor incidence from 70% to 46.7%. Taken together, the inhibitory effects of BRB on DNA damage combined with its effects on epigenetic alterations may account for BRB inhibition of oral tumorigenesis induced by DBP. Significance: We provided mechanistic insights that can account for the inhibition of oral tumors by BRB, which could serve as the framework for future chemopreventive trials for addicted smokers as well as non- or former smokers who are exposed to environmental carcinogens.

Rubusfruits are high-value crops that are sought after by consumers for their flavor, visual appeal, and health benefits. To meet this demand, production of red and black raspberries (R. idaeusL. andR. occidentalisL.), blackberries (R. subgenusRubus), and hybrids, such as Boysenberry and marionberry, is growing worldwide.Rubusbreeding programmes are continually striving to improve flavor, texture, machine harvestability, and yield, provide pest and disease resistance, improve storage and processing properties, and optimize fruits and plants for different production and harvest systems. Breeders face numerous challenges, such as polyploidy, the lack of genetic diversity in many of the elite cultivars, and until recently, the relative shortage of genetic and genomic resources available forRubus. This review will highlight the development of continually improving genetic maps, the identification of Quantitative Trait Loci (QTL)s controlling key traits, draft genomes for red and black raspberry, and efforts to improve gene models. The development of genetic maps and markers, the molecular characterization of wild species and germplasm, and high-throughput genotyping platforms will expedite breeding of improved cultivars. Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.

The alteration of white adipose tissue (WAT) &ldquo, browning&rdquo, a change of white into beige fat, has been considered as a new therapeutic strategy to treat obesity. In this study, we investigated the browning effect of black raspberry (Rubus coreanus Miquel) using in vitro and in vivo models. Black raspberry water extract (BRWE) treatment inhibited lipid accumulation in human mesenchymal stem cells (hMSCs) and zebrafish. To evaluate the thermogenic activity, BRWE was orally administered for 2 weeks, and then, the mice were placed in a 4 &deg, C environment. As a result, BRWE treatment increased rectal temperature and inguinal WAT (iWAT) thermogenesis by inducing the expression of beige fat specific markers such as PR domain zinc-finger protein 16 (PRDM16), uncoupling protein 1 (UCP1), peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1&alpha, ), and t-box protein 1 (TBX1) in cold-exposed mice. Furthermore, ellagic acid (EA), a constituent of BRWE, markedly promoted beige specific markers: UCP1, PGC1&alpha, TBX1, and nuclear respiratory factor 1 in beige differentiation media (DM)-induced 3T3-L1 adipocytes. Our findings indicate that BRWE can promote beige differentiation/activation, and EA is the active compound responsible for such effect. Thus, we suggest the nature-derived agents BRWE and EA as potential agents for obesity treatment.

Oral cancer is a public health problem with an incidence of almost 50,000 and a mortality of 10,000 each year in the USA alone. Black raspberries (BRBs) have been shown to inhibit oral carcinogenesis in several preclinical models, but our understanding of how BRB phytochemicals affect the metabolic pathways during oral carcinogenesis remains incomplete. We used a well-established rat oral cancer model to determine potential metabolic pathways impacted by BRBs during oral carcinogenesis. F344 rats were exposed to the oral carcinogen 4-nitroquinoline-1-oxide in drinking water for 14 weeks, then regular drinking water for six weeks. Carcinogen exposed rats were fed a 5% or 10% BRB supplemented diet or control diet for six weeks after carcinogen exposure. RNA-Seq transcriptome analysis on rat tongue, and mass spectrometry and NMR metabolomics analysis on rat urine were performed. We tentatively identified 57 differentially or uniquely expressed metabolites and over 662 modulated genes in rats being fed with BRB. Glycolysis and AMPK pathways were modulated during BRB-mediated oral cancer chemoprevention. Glycolytic enzymes Aldoa, Hk2, Tpi1, Pgam2, Pfkl, and Pkm2 as well as the PKA-AMPK pathway genes Prkaa2, Pde4a, Pde10a, Ywhag, and Crebbp were downregulated by BRBs during oral cancer chemoprevention. Furthermore, the glycolysis metabolite glucose-6-phosphate decreased in BRB-administered rats. Our data reveal the novel metabolic pathways modulated by BRB phytochemicals that can be targeted during the chemoprevention of oral cancer.

OBJECTIVES: Dietary strategies to reduce colonic inflammation and promote gut homeostasis may markedly reduce the risk of colitis-associated colorectal cancer. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption a Western type diet in mice. In this study, our goal was to assess the impact of consumption of the TWD with and without black raspberry supplementation on the composition of the fecal microbiome over the course of disease development. METHODS: C57BL/6 J male mice were fed a standard diet (AIN93G), the total Western diet (TWD), TWD + 5% (w/w) black raspberry powder (BRB) or TWD + 10% (w/w) BRB for 16 weeks total. After two weeks of feeding test diets, all mice were dosed with axozymethane and provided 1% dextran sodium sulfate in drinking water for 10 days to promote colonic inflammation and tumorigenesis. Composition of the fecal microbiome was determined by standard 16S rRNA sequencing following two weeks of dietary treatment, during active colitis immediately following DSS treatment and again two weeks later during the recovery period. RESULTS: Fecal microbiome profiles in mice fed diets supplemented with 5 or 10% BRB were distinct from those fed AIN93G or TWD diets, shown by significant differences in beta diversity at each of the time points (unweighted unifrac distance, permanova P

Raspberry bushy dwarf virus (RBDV), genus Idaeovirus, has been reported in commercial Rubus spp. from North and South America, Europe, Australia, New Zealand, and South Africa. Infection can cause reduced vigor and drupelet abortion leading to crumbly fruit and reduced yields (3,4). In recent years, Rubus germplasm in the form of seed, was obtained on several collection trips to The People's Republic of China to increase the diversity of Rubus spp. in the USDA-ARS National Clonal Germplasm Repository, (Corvallis, OR). Before planting in the field, seedlings were tested for the presence of RBDV, Tomato ringspot virus, and Tobacco streak virus using triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) (antiserum produced by R. R. Martin). One symptomless plant of R. multibracteatus H. Lev. & Vaniot (PI 618457 in USDA-ARS GRIN database), from Guizhou province in China, tested positive for RBDV (RBDV-China). After mechanical transmission on Chenopodium quinoa Willd., this isolate produced typical symptoms of RBDV (3). To determine if RBDV-China was a contaminant during the handling of the plants, or if the source was a seedborne virus, the coat protein gene was sequenced and compared to published sequences of RBDV. RNA was extracted from leaves of R. multibracteatus and subjected to reverse transcription-polymerase chain reaction (RT-PCR) using primers that flank the coat protein gene. Products from four separate PCR reactions were sequenced directly or were cloned into the plasmid vector pCR 2.1 (Invitrogen, Carlsbad, CA) and then sequenced. The coding sequence of the coat protein gene of RBDV-China was 87.5% (722/825) identical to that isolated from black raspberry (Genbank Accession No. s55890). The predicted amino acid sequences were 91.6% (251/274) identical. Previously, a maximum of five amino acid differences had been observed in the coat proteins of different RBDV strains (1). The 23 differences observed between RBDV-China and the isolate from black raspberry (s55890) confirm that the RBDV in R. multibracteatus is not a greenhouse contaminant but is indeed a unique strain of RBDV. In addition, monoclonal antibodies (MAbs) to RBDV (2) were tested against RBDV-China. In these tests, MAb D1 did not detect RBDV-China, whereas MAb R2 and R5 were able to detect the strain. This is the first strain of RBDV that has been clearly differentiated by MAbs using standard TAS-ELISA tests. Although RBDV is common in commercial Rubus spp. worldwide, to our knowledge, this is the first report of RBDV in R. multibracteatus, and the first report of RBDV from China. The effects of this new strain of RBDV could be more or less severe, or have a different host range than previously studied strains. It is more divergent from the type isolate than any other strain that has been studied to date. Phylogenetic analysis of coat protein genes of RBDV may be useful in understanding the evolution and spread of this virus. References: (1) A. T. Jones et al. Eur. J. Plant Pathol. 106:623, 2000. (2) R. R. Martin. Can. J. Plant. Pathol. 6:264, 1984. (3) A. F. Murant. Raspberry Bushy Dwarf. Page 229 in: Virus Diseases of Small Fruits. R. H. Converse, ed. U.S. Dep. Agric. Agric. Handb. 631, 1987. (4) B. Strik and R. R. Martin. Plant Dis. 87:294, 2003.

Blackberry chlorotic ringspot virus (BCRV), genus Ilarvirus, has been found in Rubus sp. in Scotland (2) and rose in the United States (4). The possibility that BCRV infects other hosts in the United States was explored. We tested 18 accessions of Fragaria sp. and 30 of Rubus sp. maintained at the National Clonal Germplasm Repository in Corvallis, OR. Ilarviruses had been detected in these plants by reverse transcription (RT)-PCR, ELISA, or had caused symptoms typical of ilarviruses on indicator plants. The accessions were tested by RT-PCR with primers F (5′-GTTTCCTGTGCTCCTCA-3′) and R (5′-GTCACACCGAGGTACT-3′) (4) that amplify a 519 to 522 nt (depending on the isolate) region of the RNA 3 of BCRV. The virus was detected in two accessions of black raspberry (Rubus occidentalis L.): RUB433, cv. Lowden and RUB 9012, cv. New Logan. The sequences of the fragments amplified from these accessions (GenBank Accession Nos. EF041817 and EF041818, respectively) had 97% nt sequence identity to each other and 95 and 88% nt identity to the rose and Scottish isolates (GenBank Accession Nos. DQ329378 and DQ091195, respectively). Chenopodium quinoa indicator plants inoculated with isolate RUB 433 developed mild chlorotic spots on the inoculated leaves 4 days after inoculation. RT-PCR and sequencing of the amplicons verified BCRV infection of C. quinoa. RUB 9012 was used for the characterization of Black raspberry latent virus (BRLV), later thought to be an isolate of Tobacco streak virus (TSV). This accession was recently found to be infected with Strawberry necrotic shock virus (SNSV) but not TSV (3). It is possible that BRLV may be a mixture of SNSV and BCRV. SNSV is one of the most abundant viruses of Rubus sp. in the Pacific Northwest (1), and the finding of another ilarvirus, BCRV, may account in part for the rapid decline of Rubus sp. observed in several fields in Oregon and Washington. To our knowledge, this is the first report of BCRV infecting Rubus sp. outside the United Kingdom. References: (1) A. B. Halgren. Ph.D. Diss. Oregon State University, Corvallis, OR, 2006. (2) A. T. Jones et al. Ann. Appl. Biol. 149:125, 2006. (3) I. E. Tzanetakis et al. Arch. Virol. 149:2001, 2004. (4) I. E. Tzanetakis et al. Plant Pathol. 55:568, 2006.

Erwinia amylovora causes a quarantine disease called fire blight that affects most plants from the Rosaceae family. An efficient and rapid disease diagnosis tool is needed to prevent the spread of the pathogen. The main objective of this study was to develop a lateral flow immunoassay (LFIA) to detect E. amylovora and compare different organs of plants for optimization of LFIA testing. A total of 11 strains of E. amylovora and related species were tested for specificity of the developed LFIA. The detection limit of E. amylovora was equal to 4 × 105 CFU mL−1 in plant extracts. LFIA showed high specificity and did not demonstrate positive results with non-related species. Meanwhile, LFIA's effectiveness was confirmed through testing artificially infected leaf samples of apple, pear, and black raspberry. Reliable results were obtained 10 min after the start of LFIA for all testing strains. Different plant organs (121 samples) comprising apple, pear, hawthorn, quince, blackthorn, and cherry from naturally infected areas with symptoms of varying severity were tested. The LFIA was performed using samples from leaves, twigs, flowers, fruitlets, and bacterial ooze; for confirmation commercial kits based on fluorescent amplification–based specific hybridization PCR were used. Using several samples from one plant (cluster) significantly increased the accuracy of infected plant detection, the overlap of LFIA and PCR were equal to 70.2% for individual samples and 93.5% for clusters. Observed recovery of E. amylovora for different organs differed by up to 20%. We found out that using vascular tissues was better than using leaf extracts. This result demonstrates that LFIA's effectiveness improved when more appropriate samples were used.

Bokbunja (Rubus coreanus Miquel) and six other berries were analyzed for physico-chemical properties and antioxidant activities, using four different methods (DPPH•, ABTS•+, FRAP, and reducing power). The total polyphenol, total flavonoid, and total anthocyanin contents of bokbunja were significantly higher than those of other berries, followed by mulberry, blackberry, cranberry, raspberry, wild strawberry, and strawberry. Antioxidant activity assays also showed that bokbunja’s antioxidant activity exceeded that of the other berries. Bokbunja had not only significantly higher levels of kaempferol, quercetin, and ellagic acid but also the highest ellagic acid content (408.57 mg kg−1 fresh weight). The potential antioxidant activities of bokbunja might be ascribed to its high total polyphenol, total flavonoid, and total anthocyanin contents. Ellagic acid may also affect antioxidant activity, although the concentrations of other phenolic compounds such as kaempferol, quercetin, and quercetin-3-O-rutinoside were high in other berries such as blackberry, cranberry, and mulberry.

Worldwide, cancers of the oral cavity and pharynx comprise the sixth most common malignancies. Histologically, more than 90% of oral cancers are squamous cell carcinoma (SCC). Epidemiologic data strongly support the role of exogenous factors such as tobacco, alcohol, and human papilloma virus infection as major causative agents. Avoidance of risk factors has only been partially successful, and survival rates have not improved despite advances in therapeutic approaches. Therefore, new or improved approaches to prevention and/or early detection are critical. Better understanding of the mechanisms of oral carcinogenesis can assist in the development of novel biomarkers for early detection and strategies for disease prevention. Toward this goal, several animal models for carcinogenesis in the oral cavity have been developed. Among these are xenograft, and transgenic animal models, and others employing the synthetic carcinogens such as 7,12-dimethylbenz[a]anthracene in hamster cheek pouch and 4-nitroquinoline-N-oxide in rats and mice. Additional animal models employing environmental carcinogens such as benzo[a]pyrene and N'-nitrosonornicotine have been reported. Each model has certain advantages and disadvantages. Models that (1) utilize environmental carcinogens, (2) reflect tumor heterogeneity, and (3) accurately represent the cellular and molecular changes involved in the initiation and progression of oral cancer in humans could provide a realistic platform. To achieve this goal, we introduced a novel nonsurgical mouse model to study oral carcinogenesis induced by dibenzo[a,l]pyrene (DB[a,l]P), an environmental pollutant and tobacco smoke constituent, and its diol epoxide metabolite (±)-anti-11,12-dihydroxy-13,14-epoxy-11,12,13,14-tetrahydrodibenzo[a,l]pyrene [(±)-anti-DB[a,l]PDE]. On the basis of a detailed comparison of oral cancer induced by DB[a,l]P with that induced by the other above-mentioned oral carcinogens with respect to dose, duration, species and strain, cellular and molecular targets, and relative carcinogenic potency, our animal model may offer a more realistic platform to study oral carcinogenesis. In this perspective, we also discuss our preclinical studies to demonstrate the potential of black raspberry extracts on the prevention of OSCC. Specifically, we were the first to demonstrate that black raspberry inhibited DB[a,l]P-DNA binding and of particular importance its capacity to enhance the repair of DB[a,l]P-induced bulky lesions in DNA. We believe that the information presented in this perspective will stimulate further research on the impact of environmental carcinogens in the development of oral cancer and may lead to novel strategies toward the control and prevention of this disease.

Effects of black raspberry (BRB) extract and protocatechuic acid (PCA) on DNA adduct formation and mutagenesis induced by metabolites of dibenzo[a,l]pyrene (DBP) were investigated in rat oral fibroblasts. The DBP metabolites, (±)-anti-11,12-dihydroxy-11,12,-dihydrodibenzo[a,l]pyrene (DBP-diol) and 11,12-dihydroxy-13,14-epoxy-11,12,13,14-tetrahydrodibenzo[a,l]pyrene (DBPDE) induced dose-dependent DNA adducts and mutations. DBPDE was considerably more potent, whereas the parent compound had no significant effect. Treatment with BRB extract (BRBE) and PCA resulted in reduced DBP-derived DNA adduct levels and reduced mutagenesis induced by DBP-diol, but only BRBE was similarly effective against (DBPDE). BRBE did not directly inactivate DBPDE, but rather induced a cellular response—enhanced DNA repair. When BRBE was added to cells 1 day after the DBP-diol, the BRBE greatly enhanced removal of DBP-derived DNA adducts. As oxidative stress can contribute to several stages of carcinogenesis, BRBE and PCA were investigated for their abilities to reduce oxidative stress in a human leukoplakia cell line by monitoring the redox indicator, 2′,7′-dichlorodihydrofluorescein diacetate (H2DCF) in cellular and acellular systems. BRBE effectively inhibited the oxidation, but PCA was only minimally effective against H2DCF. These results taken together provide evidence that BRBE and PCA can inhibit initiation of carcinogenesis by polycyclic aromatic hydrocarbons; and in addition, BRBE reduces oxidative stress. Cancer Prev Res; 9(8); 704–12. ©2016 AACR.

Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein-coding genes, we identified 290 very recent small-scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.

// Laura A. Kresty 1 , John J. Fromkes 2 , Wendy L. Frankel 3 , Cynthia D. Hammond 2 , Navindra P. Seeram 4 , Maureen Baird 3 , Gary D. Stoner 1 1 Division of Hematology & Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA 2 Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA 3 Department of Pathology, The Ohio State University, Columbus, Ohio, USA 4 Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA Correspondence to: Laura A. Kresty, email: Lkresty@mcw.edu Keywords: Barrett’s esophagus, black raspberry, esophageal adenocarcinoma, chemoprevention, oxidative stress Received: February 18, 2016 Accepted: May 23, 2016 Published: July 7, 2016 ABSTRACT Black raspberries inhibit a broad range of cancers in preclinical models which has led to clinical evaluations targeting premalignant lesions of the colon, oral cavity and esophagus. A phase I pilot study was conducted in twenty Barrett’s esophagus (BE) patients to investigate the effect of lyophilized black raspberries (LBR) on urinary metabolites and markers of lipid peroxidation, DNA damage and tissue markers of cellular proliferation, detoxification, and inflammation. Surveys, biopsies, blood and urine samples were collected before and after 6 months of LBR treatment (32 or 45 g). LBR significantly reduced urinary excretion of 8-epi-prostaglandin F2α, a marker of lipid peroxidation linked to oxidative stress and free radical damage. Urinary levels of the ellagitannin metabolites, urolithin A-glucuronide, urolithin A-sulfate and dimethylellagic acid glucuronide were significantly increased following 12 and 26 weeks of LBR consumption and may prove useful as indicators of compliance in future clinical studies. Immunohistochemical staining of BE biopsies following LBR treatment showed significant increases in mean GST-pi levels, with 55.6% of subjects responding favorably. In summary, LBR significantly decreased urinary lipid peroxidation levels and significantly increased GST-pi, a marker of detoxification, in BE epithelium. Still, LBR may need to be formulated differently, administered at higher concentrations or multiple times a day to increase efficacy.

The chemical characteristics of cold-pressed blackberry, black raspberry, and blueberry seed oils were evaluated for their fatty acid composition, positional distribution of fatty acids, triacylglycerol (TAG) profile, and minor component profile. The role of minor components, including tocols and pigments, on the oxidative stability was also investigated using high-temperature- and fluorescent-lighting-induced oxidation before and after tested berry seed oils were stripped of their minor components. The results indicated that all tested berry seed oils contained significant levels of palmitic (C16:0), stearic (C18:0), oleic (18:1), linoleic (C18:2ω-6), and α-linolenic (C18:3ω-3) acids, along with a favorable ratio of ω-6/ω-3 fatty acids (1.49-3.86); palmitic, stearic, oleic, and α-linolenic acids were predominantly distributed on the terminal positions. Six TAGs, namely, LnLnLn, LnLLn, LLLn, LLL, OLL, and OLLn, were the major species detected in the tested berry seed oils. Total tocol contents were 286.3-1302.9 mg/kg, which include α-, γ-, and δ-tocopherols as well as δ-tocotrienol. Oxidative stability of the three berry seed oils was compromised after the removal of tocols under high-temperature-induced oxidation, while the loss of pigments (chlorophylls) led to weak oxidative stability when exposed to fluorescent lights.

BACKGROUND: Blueberry (BB) and black raspberry (BRB) have been shown to be chemopreventive against estrogenmediated breast cancer in pre-clinical studies. However, therapeutic efficacy of these berries against lung cancer is not known. METHODS: In this study we investigated i) relative efficacy of individual anthocyanidins vs. respective anthocyanins, ii) relative antiproliferative activity of mixture of anthocyanidins compared to individual anthocyanidins, iii) antitumor activity of dietary BB, iv) Tumor inhibitory activity of diet supplemented with BB, alone and in combination with BRB, against lung tumor xenograft using nude mice, and finally, v) the efficacy of select polyphenolics present in BB and BRB against lung tumor xenograft. RESULTS: Our findings indicated that individual anthocyanidins (aglycones) were significantly more potent (2-3 fold lower IC50) in inhibiting the non-small-cell lung cancer (NSCLC) cell growth vs. respective anthocyanins (glycones). Further, anthocyanidins mixture at equimolar concentrations exhibited synergistic antiproliferative activity vs. individual anthocyanidins. When tested against NSCLC (A549 and H1299) cells in nude mice, dietary BB (7.5%, w/w) showed >40% reduction in tumor volume against H1299 xenografts. The maximal growth inhibition occurred with 5% BB dose, with no additional protection occurring at a higher dose (7.5%). However, somewhat lower protection was found when the BB diet initiated prior to tumor cell inoculation. The mixture of BB (5%, w/w) and BRB (2.5%) resulted in higher inhibition of tumor growth vs. BB alone (71% vs 42%). Likewise, a combination of delphinidin (bioactive of BB) and punicalagins (a bioactive of BRB, which gets converted to ellagic acid in vivo) showed higher tumor growth inhibition compared to delphinidin. CONCLUSIONS: The therapeutic effects of the berries and berry polyphenolics observed against lung cancer in this study are highly encouraging. Further investigation into the mechanism of action of the combinations of the berry bioactives will be valuable for clinical use of this potent natural product against lung cancer.

Rubus occidentalis (RO) has beneficial effects on glucose and lipid profiles in vitro. The aim of the study was to investigate RO extract effect on metabolic parameters in prediabetic patients, adopting a 12-week, randomized, double-blind, placebo-controlled trial. Forty-four patients (age 59.0 ± 8.2 years, 70.5% females, HbA1c 5.8 ± 0.4%) were divided into placebo (n = 13), low-dose RO extract (LRE; n = 14), or high-dose RO extract (HRE; n = 17) groups. Either 900 or 1800 mg per day of RO extract was administered orally. Area under the curve for glucose obtained 2 h after a 75-g oral glucose tolerance test was significantly decreased in the HRE group, compared with the placebo group (-28.1 ± 42.4 vs. +13.4 ± 52.6 mg/dL, p

The objective of this study was to evaluate the status of the markers related to inflammation in db/db mice fed black raspberry seed (BRS) oil, which is rich in α-linolenic acid. Mice were divided into four groups: (1) C57BL/6 mice fed 16 % calories from soybean oil (normal CON); (2) C57BL/KsJ-db/db mice fed 16 % calories from soybean oil (CON); (3) C57BL/KsJ-db/db mice fed 8 % calories from soybean and 8 % calories from BRS oil (BRS 50 %); and (4) C57BL/KsJ-db/db mice fed 16 % calories from BRS oil (BRS 100 %). After 10 weeks, n-6/n-3 fatty acid ratios were significantly (P

Demand for fresh berry products continues to grow in the United States; however, commercial raspberry production in the southeastern US is difficult because cultivars are not well adapted to the warm climate and fluctuating winter temperatures, where heat degrades plant vigor and fruit quality, and warm spells in mid to late winter can cause low chilling plants to break bud too early. Recent research about the health benefits of a polyphenolic-rich diet has led to a resurgence of interest and breeding efforts in black raspberry, and is the driving factor for this particular research. Two half-sib populations, ORUS 4304 and ORUS 4305 (307 progeny total) were planted in Jackson Springs, North Carolina in 2012. From fall 2012-spring 2015, a number of traits were measured on each plant, among them vigor, winter hardiness, and heat damage, analyzed in several different ways. Plant vigor increased or decreased over harvest seasons based on individual differences in the segregating plant population, but also showed correlations with temperature, i.e., less vigorous plants were more susceptible to damage by heat or cold. Overall, ORUS 4305 was less vigorous than ORSU 4304. As is the case with most raspberries grown in the southeast, vigor in general is expected to decrease over time; however, certain individuals show transgressive segregation for the trait. Linkage mapping for both populations is underway to identify and validate QTL for vigor, winter hardiness, heat tolerance, and other traits within black raspberry. Ultimately, we hope to gain a more complete understanding of black raspberry physiology and genetics to make breeding commercial quality cultivars a possibility in the southeast.

Administration of black raspberry (Rubus occidentalis) is known to improve vascular endothelial function in patients at a high risk for cardiovascular (CV) disease. We investigated short-term effects of black raspberry on circulating endothelial progenitor cells (EPCs) and arterial stiffness in patients with metabolic syndrome. Patients with metabolic syndrome (n = 51) were prospectively randomized into the black raspberry group (n = 26, 750 mg/day) and placebo group (n = 25) during the 12-week follow-up. Central blood pressure, augmentation index, and EPCs, such as CD34/KDR(+), CD34/CD117(+), and CD34/CD133(+), were measured at baseline and at 12-week follow-up. Radial augmentation indexes were significantly decreased in the black raspberry group compared to the placebo group (-5% ± 10% vs. 3% ± 14%, P

Objective Black raspberry (Rubus occidentalis) is known for improving vascular function. However, there has been no study evaluating its effects on 24-h systolic and diastolic blood pressure in prehypertensive patients. The aim of this study was to examine those effects. Methods Patients with prehypertension (N = 45) were prospectively randomized into a moderate-dose black raspberry group (n = 15, 1500 mg/d), a high-dose black raspberry group (n = 15, 2500 mg/d), or a placebo group (n = 15) during an 8-wk follow-up period. Raspberries were consumed in the form of a dried powder extract that was fashioned into capsules. The capsules contained 187.5 and 312.5 mg of raspberry powder, which was equivalent to 1500 and 2500 mg raspberries. Ambulatory 24-h blood pressure (BP); central BP; pulse-wave velocity; abdominal visceral fat; serum renin; angiotensin-converting enzyme; and inflammatory cytokines such as interleukin-6, tumor necrosis factor-α, C-reactive protein, soluble intercellular adhesion molecule-1, soluble vascular cell adhesion molecule-1, and plasminogen activator inhibitor-1 were measured at baseline and at 8-wk follow-up. Results High-dose black raspberry significantly reduced 24-h systolic blood pressure (SBP; 3.3 ± 10 mm Hg versus –6.7 ± 11.8 mm Hg; P

A high concentration of histamine, one of the biogenic amines (BAs) usually found in fermented foods, can cause undesirable physiological side effects in sensitive humans. The objective of this study is to isolate indigenous Acetobacter strains from naturally fermented Bokbunja vinegar in Korea with reduced histamine production during starter fermentation. Further, we examined its physiological and biochemical properties, including BA synthesis. The obtained strain MBA-77, identified as Acetobacter aceti by 16S rDNA homology and biochemical analysis and named A. aceti MBA-77. A. aceti MBA-77 showed optimal acidity % production at pH 5; the optimal temperature was 25 °C. When we prepared and examined the BAs synthesis spectrum during the fermentation process, Bokbunja wine fermented with Saccharomyces cerevisiae showed that the histamine concentration increased from 2.72 of Bokbunja extract to 5.29 mg/L and cadaverine and dopamine was decreased to 2.6 and 10.12 mg/L, respectively. Bokbunja vinegar prepared by A. aceti MBA-77 as the starter, the histamine concentration of the vinegar preparation step was decreased up to 3.66 mg/L from 5.29 mg/L in the wine preparation step. To our knowledge, this is the first report to demonstrate acetic acid bacteria isolated from Bokbunja seed vinegar with low spectrum BA and would be useful for wellbeing vinegar preparation.

A major challenge for the food industry is to satisfy the consumer demand for health benefits as well as taste. In this study, we investigated the antioxidant activities of extracts from four anthocyanin-rich jams, as well as their low-sugar versions, which used white grape juice concentrate as a white refined sugar substitute. It was determined that blueberry + Korean black raspberry jam dramatically scavenged 1,1-diphenyl-2-picrylhydrazyl, 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid), peroxyl radicals, and reduced ferric ions in the tested jams and contained high amounts of phenols, flavonoids, and anthocyanins. In addition, the antioxidant capacity and content of phenolics, flavonoids, and anthocyanins were retained during the processing of berry jams. Berry jams and their low-sugar jams exhibited inhibitory effects on reactive oxygen species production in HepG2 cells and lipid peroxidation in the liver and brain homogenates. In conclusion, blueberry + Korean black raspberry and raspberry + strawberry jams have strong antioxidant capacities, which are retained in jams containing sugar substitutes. These results suggest that anthocyanin-rich berry jams with natural sugar replacements could be developed as high functional foods and also decrease the risk for metabolic diseases.

Black raspberries (BRB) demonstrate potent inhibition of aerodigestive tract carcinogenesis in animal models. However, translational clinical trials evaluating the ability of BRB phytochemicals to impact molecular biomarkers in the oral mucosa remain limited. The present phase 0 study addresses a fundamental question for oral cancer food–based prevention: Do BRB phytochemicals successfully reach the targeted oral tissues and reduce proinflammatory and antiapoptotic gene expression profiles? Patients with biopsy-confirmed oral squamous cell carcinomas (OSCC) administered oral troches containing freeze-dried BRB powder from the time of enrollment to the date of curative intent surgery (13.9 ± 1.27 days). Transcriptional biomarkers were evaluated in patient-matched OSCCs and noninvolved high at-risk mucosa (HARM) for BRB-associated changes. Significant expression differences between baseline OSCC and HARM tissues were confirmed using a panel of genes commonly deregulated during oral carcinogenesis. Following BRB troche administration, the expression of prosurvival genes (AURKA, BIRC5, EGFR) and proinflammatory genes (NFKB1, PTGS2) were significantly reduced. There were no BRB-associated grade 3–4 toxicities or adverse events, and 79.2% (N = 30) of patients successfully completed the study with high levels of compliance (97.2%). The BRB phytochemicals cyanidin-3-rutinoside and cyanidin-3-xylosylrutinoside were detected in all OSCC tissues analyzed, demonstrating that bioactive components were successfully reaching targeted OSCC tissues. We confirmed that hallmark antiapoptotic and proinflammatory molecular biomarkers were overexpressed in OSCCs and that their gene expression was significantly reduced following BRB troche administration. As these molecular biomarkers are fundamental to oral carcinogenesis and are modifiable, they may represent emerging biomarkers of molecular efficacy for BRB-mediated oral cancer chemoprevention. Cancer Prev Res; 9(2); 159–71. ©2015 AACR.

BACKGROUND The aim of this study was to elucidate the changes in microbial community and biochemical and physiological properties of traditional Muju black raspberry (Robus coreanus Miquel) vinegar (TMBV) during fermentation by culture-independent methods. RESULTS During vinegar fermentation, ethanol produced up to 120 g L−1 until day 35, with continuously increasing yeast concentration to a total of log 7.6 CFU mL−1. After day 35, acetic acid bacteria (AAB) concentrations rose to log 5.8 CFU mL−1 until day 144. Denaturing gradient gel electrophoresis analysis showed that Saccharomyces cerevisiae was detected until day 87 of the fermentation, at which point Acetobacter pasteurianus gradually took over as the dominant species. Total sugar was reduced to 6.6 °Brix and total acidity produced up to 44 g L−1. CONCLUSION In this study, we established the physicochemical analysis and growth dynamics of yeast and AAB during alcoholic and acetic acid fermentation of black raspberry by a traditional method. Overall, S. cerevisiae and A. pasteurianus species appeared to dominate the TMBV fermentation. In conclusion, this study demonstrated a suitable fermentation system for TMBV by the static surface method. © 2015 Society of Chemical Industry

Background: Fruits are considered one of the richest sources of natural antioxidants. Their consumption has been linked to the prevention of oxidative stress-induced diseases. Objective: In this study, in vitro antioxidant activities of blueberry, jackfruit, blackberry, black raspberry, red raspberry, strawberry, and California table grape extracts were evaluated. Materials and Methods: Antioxidant activities were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant potential (FRAP), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), nitric oxide (NO), superoxide anion (O2−) scavenging assays, and ferric reducing power. Results: Black raspberry extract had the highest phenolic (965.6 ± 2.9 mg gallic acid equivalents [GAE]/g), flavonoid (186.4 ± 1.7 mg quercetin equivalents/g), and proanthocyanidin (2677 ± 71.1 mg GAE/g) contents. All fruit extracts exhibited increasing radical scavenging activities with increased concentrations. At 100 μg/ml, red raspberry extract showed the highest ferric reducing power (A700 =0.3 ± 0.0052) and FRAP activity (A593 =11.43 mM Fe2+/g). Black raspberry extract (100 μg/ml) exhibited the highest DPPH activity (A517 =89.03 ± 0.0471). Jackfruit extract (100 μg/ml) had the highest ABTS (A734 =35.6 ± 0.613), NO (A540 =81.7 ± 0.2), and O2− radical scavenging (A230 =55.5 ± 0.2) activities. Positive correlations were observed between IC50 values for different radical scavenging activities and different polyphenolics. Red raspberry extract had the highest Pearson's coefficient values (0.952–1) between total phenolics, flavonoids, and proanthocyanidins and DPPH and superoxide radical scavenging activities. Conclusions: The antioxidant rich fruits in this study are good source of functional food and nutraceuticals that have the potential to improve human health. SUMMARY All fruit extracts exhibited increasing radical scavenging activities with increased concentrationsBlack raspberry extract is enriched in total phenols, flavonoids, and proanthocyanidins and showed the highest 2,2-diphenyl-1-picrylhydrazyl scavenging activity and red raspberry extract showed the highest ferric reducing power and ferric reducing antioxidant potential activityJackfruit extract exhibited the highest 2,2′azino-bis (3-ethylbenzothiazoline-6-sulfonicacid) diammonium salt, nitric oxide, O2- scavenging activitiesPositive correlations were observed between IC50 values for different radical scavenging activities and different polyphenolics. Abbreviations Used: Abs: Absorbance, ABTS: 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt, BHT: Butylated hydroxytoluene, DPPH: 2,2-diphenyl-1-picrylhydrazyl, DW: Dry weight, FRAP: Ferric reducing antioxidant potential, FW: Fresh weight, GAE: Gallic acid equivalents, NADH: β-nicotinamide adenine dinucleotide hydrate, NFL: The National Food Laboratories, NO: Nitric oxide, ONPG: ortho-nitrophenyl-β-galactoside, PBS: Phosphate buffered saline, PMS: Phenazine methosulfate, QE: Quercetin equivalents, ROS: Reactive oxygen species, SD: Standard deviation, SOD: Superoxide dismutase, TCA: Trichloroacetic acid, TPTZ: 2,4,6-tris(2-pyridyl)-s-triazine, Trolox: (±)-6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid.

Contact hypersensitivity (CHS) is the most common occupational dermatological disease. Dendritic cells (DCs) mediate the sensitization stage of CHS, while T-cells facilitate the effector mechanisms that drive CHS. Black raspberry (Rubus occidentalis, BRB) and BRB phytochemicals possess immunomodulatory properties, but their dietary effects on CHS are unknown. We examined the effects of diets containing BRB and protocatechuic acid (PCA, a constituent of BRB and an anthocyanin metabolite produced largely by gut microbes), on CHS, using a model induced by 2,4-dinitrofluorobenze (DNFB). Mice were fed control diet or diets supplemented with BRB or PCA. In vitro bone-marrow derived DCs and RAW264.7 macrophages were treated with BRB extract and PCA. Mice fed BRB or PCA supplemented diets displayed decreased DNFB-induced ear swelling, marked by decreased splenic DC accumulation. BRB extract diminished DC maturation associated with reduced Cd80 expression and Interleukin (IL)-12 secretion, and PCA reduced IL-12. Dietary supplementation with BRB and PCA induced differential decreases in IL-12-driven CHS mediators, including Interferon (IFN)-&gamma, and IL-17 production by T-cells. BRB extracts and PCA directly attenuated CHS-promoting macrophage activity mediated by nitric oxide and IL-12. Our results demonstrate that BRB and PCA mitigate CHS pathology, providing a rationale for CHS alleviation via dietary supplementation with BRB or BRB derived anthocyanins.

Metabolic syndrome is characterized by a combination of several metabolic disorders, including obesity, hyperglycemia, and hyperlipidemia. A simultaneous occurrence is one of the most crucial features of metabolic syndrome, therefore, we selected an animal model in which this would be reflected. We fed C57BL/6N mice a high-fat diet for 23 weeks to develop metabolic syndrome and examined the efficacy of Rubus occidentalis (RO) for hyperglycemia and hypercholesterolemia. Oral administration of RO for 16 weeks improved hyperglycemia as indicated by significantly decreased fasting glucose levels and a glucose tolerance test. Improvements were also observed in hypercholesterolemia, in which significant decreases in serum total cholesterol, non-high-density lipoprotein (non-HDL) cholesterol, apolipoprotein A-1, and apolipoprotein B levels were observed. The time comparison of major biomarkers, observed at the initiation and termination of the experimental period, consistently supported the beneficial effects of RO on each metabolic phenotype. In addition, RO treatment attenuated the excessive fat accumulation in hepatic and adipose tissue by decreasing the size and number of lipid droplets. These results suggested that RO simultaneously exerted antihyperglycemic and antihyperlipidemic effects in mice with diet-induced metabolic syndrome.

Berries have been used as valuable sources of polyphenols for human health; however, injudicious uses of berries are widespread without regard to the specific metabolite constituent of each berry. We classified 6 different edible berries (honeyberry, blueberry, mandarin melonberry, mulberry, chokeberry, and Korean black raspberry) based on their metabolite distributions in biosynthetic pathways by non-targeted metabolite profiling and bioactive correlation analysis. Principal component analysis revealed a distinct clustering pattern of metabolites for each berry. Metabolic pathway analysis revealed different biosynthetic routes of secondary metabolites in each berry. Mandarin melonberry contains a relatively higher proportion of genistein, genistein glycoside, and genistein-derived isoflavonoids and prenylflavonoids than the other berries. Various anthocyanin glycosides, synthesized from dihydroquercetin and cyanidin, were more abundant in chokeberry and honeyberry, whereas high levels of flavonoid-and anthocyanins-rutinoside forms were observed in Korean black raspberry. The levels of anthocyanins derived from dihydromyricetin were high in blueberry. The highest anti-oxidant activity was observed in chokeberry and Korean black raspberry, which is positively related to the proportional concentration of flavonoids, phenolics, and anthocyanins. The lowest sugar contents were observed in Korean black raspberry, highest acidity in honeyberry, and lowest acidity in mandarin melonberry, which were specific characteristics among the berries. Taken together, biosynthetic pathway and physicochemical characteristics analyses revealed that the different synthesized routes of flavonoids and anthocyanins and associated bio-activities may be distinct features in each berry and explain their phenotypic diversity at the molecular level.

Background The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Findings Here, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. Conclusions The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.

The objective of this study was to evaluate probiotic effects of two Lactobacillus plantarum strains (GBL16 and 17) isolated from black raspberry. Results revealed that the number of GBL16 was gradually decreased as bile salt concentration was increased from 0.3 to 1%. However, GBL17 did not show any difference when GBL17 was applied to 1% bile salt, and it indicates that GBL17 is more tolerant to bile salt than GBL16. GBL17 exhibited higher heat resistance and adhesion ability to Caco-2 cells than GBL16. Regarding gut microbiome, no significant change in the number of total bacteria in intestines of mice after treatment with GBLs was determined. However, the combination of GBL16 and GBL17 significantly increased the number of total bacteria in intestines of mice after they were orally administered. Therefore, the results suggest that both GBL16 and 17 strains could be one of major probiotics that can improve human gut health.