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Abstract Elucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predicting gene expression profiles from gene flanking regions of the plant species Arabidopsis thaliana, Solanum lycopersicum, Sorghum bicolor, and Zea mays. With over 80% accuracy, our models enabled predictive feature selection, highlighting e.g. the significant role of UTR regions in determining gene expression levels. The models demonstrated remarkable cross-species performance, effectively identifying both conserved and species-specific regulatory sequence features and their predictive power for gene expression. We illustrated the application of our approach by revealing causal links between genetic variation and gene expression changes across fourteen tomato genomes. Lastly, our models efficiently predicted genotype-specific expression of key functional gene groups, exemplified by underscoring known phenotypic and metabolic differences between Solanum lycopersicum and its wild, drought-resistant relative, Solanum pennellii.

The phase I enzyme known as cytochrome P450 1B1 (CYP1B1) is involved in the metabolism of many endogenous and exogenous compounds, including carcinogens. CYP1B1 is overexpressed in a wide variety of human diseases ranging from diabetes to malignancies, such as invasive breast cancer. Because of its microsomal location in the cell, CYP1B1 could not be measured directly by existing methods but only assessed indirectly via the determination of the catalytic products. We report here a rapid, sensitive piezoimmunosensor for detection of CYP1B1 using single-chain fragment variable antibodies (scFv) as recognition elements and a quartz crystal microbalance (QCM) as the transducer. Three anti-CYP1B1 scFvs (designated B-66, D-23, and L-21) were biotinylated and used to capture and specifically detect CYP1B1 from samples in solution. ScFvs are smaller than most commonly used antibodies and can be coated onto QCM surfaces at much higher density to improve sensor sensitivity and specificity. The scFv-QCM biosensors showed excellent sensitivity (detection limit, 2.2 [+ or -] 0.9 nM) and specificity with a dissociation constant [K.sub.d] = (1.54 [+ or -] 0.59) x [10.sup.-7] M. CYP1B1 were quantitatively detected in normal and malignant cell lysates (e.g., human T47D breast cancer cell microsomes). Results demonstrate that an anti-CYP1B1 scFv-QCM immunosensor could be used to detect P450 enzymes in biological samples.

Hydrogen-terminated diamond is known for its unusually high surface conductivity that is ascribed to its negative electron affinity. In the presence of acceptor molecules, electrons are expected to transfer from the surface to the acceptor, resulting in p-type surface conductivity. Here, we present Kelvin probe force microscopy (KPFM) measurements on carbon nanotubes and C60 adsorbed onto a hydrogen-terminated diamond(001) surface. A clear reduction in the Kelvin signal is observed at the position of the carbon nanotubes and C60 molecules as compared with the bare, air-exposed surface. This result can be explained by the high positive electron affinity of carbon nanotubes and C60, resulting in electron transfer from the surface to the adsorbates. When an oxygen-terminated diamond(001) is used instead, no reduction in the Kelvin signal is obtained. While the presence of a charged adsorbate or a difference in work function could induce a change in the KPFM signal, a charge transfer effect of the hydrogen-terminated diamond surface, by the adsorption of the carbon nanotubes and the C60 fullerenes, is consistent with previous theoretical studies. [ABSTRACT FROM AUTHOR]

People with a mutation in the gene for the melanocortin 4 receptor may engage in binge eating, which could explain why this gene mutation has been linked with obesity. In a study of 494 people, all 24 obese people with this mutation reported binge eating compared to 14% of obese people without the mutation and none of the 25 normal-weight men and women. This receptor is the receptor for a hormone that controls appetite.

Women with a fibroadenoma appear to be at an increased risk of developing breast cancer. Fibroadenomas are benign breast tumors, usually diagnosed in young women. The long-term medical records and biopsy specimens of 1,835 women with fibroadenomas were compared to those from a control group of women without fibroadenomas. Those with fibroadenoma were 2.1 times more likely to develop breast cancer. Those with one of the complex manifestations of the tumor were 3.1 times more likely to develop breast cancer. A family history of breast cancer raised the relative risk to 3.72 for women diagnosed with a complex fibroadenoma.