Identification of unknown genetically modified material admixed in conventional cotton seed and development of an event-specific detection method

Entering the second decade of commercialization of biotech crops, the global area cultivated with transgenic plants constantly expands and national legislations in many countries, particularly in the European Union, require identification and labeling of genetically modified material in food and feed. We describe here a procedure for characterizing transgenic material of unknown origin present in conventional seed lots using a genome walking strategy for isolation and characterization of the junction between the inserted transgene construct and the host plant genomic DNA. The procedure was applied to transgenic cotton detected as adventitious or technically unavoidable presence in a conventional commercial cultivar. The structure of the isolated region revealed that the transgenic material derived from Monsanto’s event 1445 transgenic cotton. Due to the random incorporation of the transgene into the host plant’s genome, the sequence of the junction region obtained using the genome walking strategy, provided the means to develop an event-specific identification method without prior knowledge for the nature of the transformation event. Thus, we documented a methodology for developing an event-specific detection protocol even without prior knowledge of the genetic modification event

A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream (Sparus aurata) originating from fish farms from two geographically distinct areas of Greece

Bacterial diversity of whole gilt-head sea bream (Sparus aurata L. 1758) originating from Ionian and Aegean Sea aquaculture farms and stored at 0 (ice), 4 and 8 °C was determined by 16S rRNA gene amplicon sequencing method using the Illumina's MiSeq platform. The composition of Aerobic Plate Counts (APC) was also monitored by 16S rRNA gene sequencing. The rejection time point of sea bream from either area, as determined by sensory evaluation, was about 14, 6 and 3 days at 0, 4 and 8 °C, respectively. APC was approximately 4.5 log cfu/g at day 0 and ranged from 7.5 to 8.5 log cfu/g at sensory rejection. Culture-depended analysis showed that Pseudomonas and Shewanella were the most abundant microorganisms grown on plates for both seas. Moreover, culture-independent analysis of DNA extracted directly from fish flesh showed that sea bream originating from different geographical areas exhibited different bacterial diversity. Pseudomonas and Psychrobacter were the dominant microorganisms of chill-stored fish from Ionian (apart from 8 °C, where Carnobacterium dominated) and Aegean Sea, respectively. In addition, small changes of storage temperature greatly affected bacterial microbiota of stored fish. Various bacterial species, not detected by conventional microbiological methods, were also revealed through 16S amplicon sequencing. In conclusion, the use of NGS approach is a promising methodology for assessing bacterial diversity of sea bream originating from different geographical areas and stored at various temperatures. © 201

Bacterial communities and potential spoilage markers of whole blue crab (Callinectes sapidus) stored under commercial simulated conditions

Bacterial communities composition using 16S Next Generation Sequencing (NGS) and Volatile Organic Compounds (VOCs) profile of whole blue crabs (Callinectes sapidus) stored at 4 and 10 °C (proper and abuse temperature) simulating real storage conditions were performed. Conventional microbiological and chemical analyses (Total Volatile Base-Nitrogen/TVB-N and Trimethylamine-Nitrogen/TMA-N) were also carried out. The rejection time point was 10 and 6 days for the whole crabs stored at 4 and 10 °C, respectively, as determined by development of unpleasant odors, which coincided with crabs death. Initially, the Aerobic Plate Count (APC) was 4.87 log cfu/g and increased by 3 logs at the rejection time. The 16S NGS analysis of DNA extracted directly from the crab tissue (culture-independent method), showed that the initial microbiota of the blue crab mainly consisted of Candidatus Bacilloplasma, while potential pathogens e.g. Listeria monocytogenes, Pseudomonas aeruginosa and Acinetobacter baumannii, were also found. At the rejection point, bacteria of Rhodobacteraceae family (52%) and Vibrio spp. (40.2%) dominated at 4 and 10 °C, respectively. TVB-N and TMA-N also increased, reaching higher values at higher storage temperature. The relative concentrations of some VOCs such as 1-octen-3-ol, trans-2-octenal, trans,trans-2,4-heptadienal, 2-butanone, 3-butanone, 2-heptanone, ethyl isobutyrate, ethyl acetate, ethyl-2-methylbutyrate, ethyl isovalerate, hexanoic acid ethyl ester and indole, exhibited an increasing trend during crab storage, making them promising spoilage markers. The composition of microbial communities at different storage temperatures was examined by 16S amplicon meta-barcoding analysis. This kind of analysis in conjugation with the volatile profile can be used to explore the microbiological quality and further assist towards the application of the appropriate strategies to extend crab shelf-life and protect consumer's health. © 201

Microbial spoilage investigation of thawed common cuttlefish (Sepia officinalis) stored at 2 °C using next generation sequencing and volatilome analysis

Cephalopods are highly appreciated with increasing demand seafood, but are also very perishable and deteriorate fast mainly due to microbiological spoilage. For this reason exploration of bacterial communities through 16S Next Generation Sequencing (NGS) and Volatile Organic Compounds (VOCs) analysis was performed. Furthermore, sensory evaluation, classical microbiological analysis, Total Volatile Base-Nitrogen/TVB-N and Trimethylamine-Nitrogen/TMA-N determination were also carried out. Shelf-life of thawed cuttlefish (Sepia officinalis) stored at 2°C determined by sensory evaluation was 4 days. Aerobic Plate Counts (APC) reached the levels of 6.6 log cfu/g. The initial and final population of all spoilage microorganisms enumerated with selective media was under detectable levels with the exception of Pseudomonas. Based on 16S NGS analysis, Psychrobacter were the dominants among others, e.g. Pseudomonas, Shewanella, Comamonas, Carnobacterium, Vagococcus, of the initial microbiota. Psychrobacter was also the dominant microorganisms of the spoiled cuttlefish. TVB-N and TMA-N increased considerably only at the late stages of storage. A plethora of VOCs were produced and some exhibited an increasing profile throughout storage, making them promising molecules as freshness indicators in contrast to TVB-N and TMA-N. The application of next generation sequencing revealed the microbiota that escapes the classic microbiological methodologies, showing that other microorganisms different from those determined on selective culture media might be the main cause of microbiological spoilage. © 201

Acceptability of Self-Sampling for Human Papillomavirus-Based Cervical Cancer Screening

Background: Human papillomavirus (HPV)-DNA testing combined with self-sampling could increase cervical cancer screening effectiveness, utilizing a sensitive screening modality and an easy sampling method with minimal pain or discomfort. Self-sampling acceptability, though, is pivotal. Materials and Methods: This study is a nested cross-sectional survey within GRECOSELF, a cross-sectional study on HPV-based screening with self-sampling, aiming at investigating self-sampling acceptability among Greek women residing in rural areas, and the factors affecting it. Women between 25 and 60 years old were recruited by midwives participating in a nationwide midwifery network. Participants, after self-sampling, filled out a questionnaire with three sections, one regarding demographic characteristics, a second with questions pertaining to the participants' cervical cancer screening history, and a third with questions regarding the self-sampling process per se. Results: The sample included 13,111 women. Most participants (67.9%), including those screened or not in the past, would prefer self-sampling if assured that the results are not inferior to standard testing. Discomfort or pain during self-sampling was absent or minimal in 97.1% and 96.5% of the cases, respectively, and 74.4% of the women felt adequately confident that they followed the instructions correctly. Women mostly preferred self-sampling at home compared with health care facilities. Pain and discomfort during the procedure, although rare, were significant factors against acceptance. Most of the women reporting a negative impression had a negative experience with conventional sampling in the past. Conclusion: Self-sampling is highly acceptable. Acceptance can be further improved with proper communication of the process and its noninferiority compared with conventional screening. © Copyright 2020, Mary Ann Liebert, Inc., publishers 2020

Acceptability of Self-Sampling for Human Papillomavirus-Based Cervical Cancer Screening

Background: Human papillomavirus (HPV)-DNA testing combined with self-sampling could increase cervical cancer screening effectiveness, utilizing a sensitive screening modality and an easy sampling method with minimal pain or discomfort. Self-sampling acceptability, though, is pivotal. Materials and Methods: This study is a nested cross-sectional survey within GRECOSELF, a cross-sectional study on HPV-based screening with self-sampling, aiming at investigating self-sampling acceptability among Greek women residing in rural areas, and the factors affecting it. Women between 25 and 60 years old were recruited by midwives participating in a nationwide midwifery network. Participants, after self-sampling, filled out a questionnaire with three sections, one regarding demographic characteristics, a second with questions pertaining to the participants' cervical cancer screening history, and a third with questions regarding the self-sampling process per se. Results: The sample included 13,111 women. Most participants (67.9%), including those screened or not in the past, would prefer self-sampling if assured that the results are not inferior to standard testing. Discomfort or pain during self-sampling was absent or minimal in 97.1% and 96.5% of the cases, respectively, and 74.4% of the women felt adequately confident that they followed the instructions correctly. Women mostly preferred self-sampling at home compared with health care facilities. Pain and discomfort during the procedure, although rare, were significant factors against acceptance. Most of the women reporting a negative impression had a negative experience with conventional sampling in the past. Conclusion: Self-sampling is highly acceptable. Acceptance can be further improved with proper communication of the process and its noninferiority compared with conventional screening. © Copyright 2020, Mary Ann Liebert, Inc., publishers 2020

Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) stereotyped subsets #6 and #8 include cases expressing unmutated B cell receptor immunoglobulin (BcR IG) (U-CLL). Subset #6 (IGHV1-69/IGKV3-20) is less aggressive compared to subset #8 (IGHV4-39/IGKV1(D)-39) which has the highest risk for Richter's transformation among all CLL. The underlying reasons for this divergent clinical behavior are not fully elucidated. To gain insight into this issue, here we focused on epigenomic signatures and their links with gene expression, particularly investigating genome-wide DNA methylation profiles in subsets #6 and #8 as well as other U-CLL cases not expressing stereotyped BcR IG. We found that subset #8 showed a distinctive DNA methylation profile compared to all other U-CLL cases, including subset #6. Integrated analysis of DNA methylation and gene expression revealed significant correlation for several genes, particularly highlighting a relevant role for the TP63 gene which was hypomethylated and overexpressed in subset #8. This observation was validated by quantitative PCR, which also revealed TP63 mRNA overexpression in additional nonsubset U-CLL cases. BcR stimulation had distinct effects on p63 protein expression, particularly leading to induction in subset #8, accompanied by increased CLL cell survival. This pro-survival effect was also supported by siRNA-mediated downregulation of p63 expression resulting in increased apoptosis. In conclusion, we report that DNA methylation profiles may vary even among CLL patients with similar somatic hypermutation status, supporting a compartmentalized approach to dissecting CLL biology. Furthermore, we highlight p63 as a novel prosurvival factor in CLL, thus identifying another piece of the complex puzzle of clinical aggressiveness. What's new? In chronic lymphocytic leukemia (CLL), cases with unmutated immunoglobulin receptors (U-CLL) are generally associated with inferior outcome, albeit still displaying considerable heterogeneity. Might such differences in CLL progression be explained by epigenetics? In this study, the authors found that an unusually aggressive subset of CLLs called subset #8 has a distinctive DNA-methylation profile. They also found that p63 is a novel pro-survival factor for CLL cells. These molecular studies may lead to new prognostic biomarkers, and possibly new therapeutic targets, for CLL