Utilization of specific primers in legume allergens based polymorphism screening

Different types of allergies became a part of life of many people around the world. The research activities connecting to allergens are actually not oriented only for protein and immunological interactions, but to the genomic and transcriptomic background of them, too. Analysis and description of genomic variability of allergens in plant food resources will help to manage the allergen based strategies in the future. Here, the bioinformatic approach was used to develop and validate the specific primers for genomic screening of polymorphism of profilins (Profilin Based Amplicon Polymorphism; PBAP) and vicilins (Vicilin Based Amplicon Polymorphism; VBAP) among the legumes. The alignment of existing public databases data for these allergens in the group of legumes was performed. Subsequently, specific primers were designed and their ability to generate polymorphic amplicons were tested for three legumes – bean, lentil and chickpeas. In all cases, amplicons were generated and polymorphism was detected in all three species for profilin as well as for vicilin.

Loss-of-Function FLNC Variants are Associated with Arrhythmogenic Cardiomyopathy Phenotypes when Identified through Exome Sequencing of a General Clinical Population

Background The FLNC gene has recently garnered attention as a likely cause of arrhythmogenic cardiomyopathy (ACM), which is considered an actionable genetic condition. However, the association with disease in an unselected clinical population is unknown. We hypothesized that individuals with loss-of-function variants in FLNC (FLNCLOF) would have increased odds for ACM-associated phenotypes versus variant-negative controls in the Geisinger MyCode cohort. Methods We identified rare, putative FLNCLOF among 171,948 individuals with exome sequencing linked to health records. Associations with ACM phenotypes from available diagnoses and cardiac evaluations were investigated. Results Sixty individuals (0.03%; median age 58 years [47 — 70 IQR], 43% male) harbored 27 unique FLNCLOF. These individuals had significantly increased odds ratios (OR) for dilated cardiomyopathy (OR:4.9, [95% confidence interval: 2.6 — 7.6]; p<0.001), supraventricular tachycardia (OR:3.2, [1.1 — 5.6]; p=0.01), defibrillator implantation (OR:4.6, [1.9 — 8.4]; p<0.001), and left-dominant ACM (OR:4.2, [1.4 — 7.9]; p=0.003). Echocardiography revealed reduced left ventricular ejection fraction (52 ± 13% vs. 57 ± 9%; p=0.001) associated with FLNCLOF. Overall, at least 9% of FLNCLOF carriers demonstrated evidence of penetrant disease. Conclusions FLNCLOF variants are associated with increased odds of ventricular arrhythmia and dysfunction in an unselected clinical population. These findings support genomic screening of FLNC for actionable secondary findings.

Ethics, Data and Information in Genome Sequencing in Newborns

"One of the current debates in Genetics is the genomic sequencing in newborns. Thanks to the genomic technologies, it is currently possible to detect diseases that a newborn may suffer in the short, medium or long term. Genomic tests pose some important ethical issues. Those issues can be classified in three different types: those regarding the object of the screening (genes that must be analyzed), those related to the information (how it must be managed) and those regarding justice questions (economic costs, population to be included in some screening programs). This study is based on a previous study whose aim was to present a general view of those three ethical problems. This study aims to focus on one of these three problems: the information. We think that how to manage the information on the results of a genomic sequencing in newborns is perhaps the most important ethical issue in this topic. Hence this work aims to address these questions regarding information on genomic sequencing: How the genomic screening has to be explained to the parents in order to get the informed consent? Should the physician give them all the data or only the information related to some genes about which he is sure that they will cause a disease? How the genomic information has to be managed? Can we keep this information once we have finished the screening of a newborn? Should we destroy it after the screening? Is it ethical that parents, without a prescription or medical control, can do on their own a genomic screening on their newborn child? "

Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere

Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the ‘opportunistic’ behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.

Optimized Cas9 expression improves performance of large-scale CRISPR screening

CRISPR technology is an invaluable tool for large-scale functional genomic screening. Genome editing efficiency and timing are important parameters impacting the performance of pooled CRISPR screens. Here we show that by optimizing Cas9 expression levels, the time necessary for gene editing can be reduced contributing to improved performance of CRISPR based screening.