Biology subjects

Sadeh, R.

Publications and source records attributed to Sadeh, R..

4 recordsLinked to original sources

bioRxiv2023

Optimization of chickpea irrigation in a semi-arid climate based on morpho-physiological parameters

While the world population is steadily growing, the demand for plant-based protein in general, and chickpea in particular, is rising. Heatwaves and terminal drought are the main environmental constraints on chickpea production worldwide. Thus, developing better irrigation management for the chickpea agro-system can promote higher and more sustainable yields. Supplemental irrigation at the right timing and dose can increase yield dramatically. Here, we studied the response of a modern Kabuli chickpea cultivar to supplemental irrigation during the critical pod-filling period over three growing seasons (2019-2021) in northern Negev, Israel, under semi-arid conditions. Six irrigation treatments were applied based on irrigation factors of 0, 0.5, 0.7, 1.0, 1.2, and 1.4 of crop evapotranspiration (ET0) as measured by an on-site meteorological station. Morpho-physiological parameters and above-ground biomass accumulation were monitored throughout the cropping seasons, and the final grain yield was determined at maturation. Irrigation onset was determined based on plants leaf water potential ({Psi}LWP > 15 bar) in the field. Our results indicate that optimal water status (as reflected by pressure chamber values) was 12-14 bar during the irrigation period. Irrigation according to evapotranspiration (ET0) with an irrigation factor of 1.2 resulted in the highest grain yields over the three years. To ensure optimal water supply during the reproductive phase compatible with the crop water requirements, maintaining a 25 mm node length above the last fully developed pod and a 90 mm distance between the last fully developed pod to the stem apex is recommended. In conclusion, irrigation onset when the crop is already at mild drought stress, followed by sufficient irrigation while following the indicated morphology and water potential values, may help farmers optimize irrigation and maximize chickpea crop production. HighlightsO_LIChickpea irrigation is optimized based on meteorological data (ETc) and morphological traits. C_LIO_LIMorphological- not only physiological- traits can capture the dynamics of crop water status. C_LIO_LIIrrigation onset should be at mild drought stress (>15 bar) during the reproductive stage. C_LIO_LIExtending the reproductive phase is essential for grain yield improvement under semi-arid conditions. C_LIO_LIIF=1.2 provides the most productive irrigation regime for chickpea in Mediterranean conditions. C_LI

plant biology↗

bioRxiv2022

Subtyping of Small Cell Lung Cancer using plasma cell-free nucleosomes

Emerging data on small cell lung cancer (SCLC), an aggressive malignancy with exceptionally poor prognosis, support subtypes driven by distinct transcription regulators, which engender unique therapeutic vulnerabilities. However, the translational potential of these observations is limited by access to tumor biopsies. Here, we leverage chromatin immunoprecipitation of cell-free nucleosomes carrying active chromatin modifications followed by sequencing (cfChIP-seq) on 442 plasma samples from individuals with advanced SCLC, neuroendocrine carcinomas (NEC), non-SCLC cancers, and healthy adults. Beyond providing reliable estimates of SCLC circulating free DNA tumor fraction, cfChIP-seq captures the unique epigenetic states of SCLC tissue- and cell-of-origin. Comparison of cfChIP-seq signals to matched tumor transcriptomes reveals genome-wide concordance, establishing a direct link between gene expression in the tumor and plasma cell-free nucleosomes. Exploiting this link, we develop a classifier that discriminates between SCLC lineage-defining transcription factor subtypes based on cfChIP-seq data. This work sets the stage to non-invasively profile SCLC transcriptomes using plasma cfDNA histone modifications.

cancer biology↗

bioRxiv2019

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

AbstractGenomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test. One Sentence SummaryChIP-seq of plasma-circulating nucleosomes (cfChIP-seq) from a simple blood test provides detailed information about gene expression programs in human organs, and cancer.

molecular biology↗

bioRxiv2017

Deciphering cis-regulatory logic with 100 million synthetic promoters

Deciphering cis-regulation, the code by which transcription factors (TFs) interpret regulatory DNA sequence to control gene expression levels, is a long-standing challenge. Previous studies of native or engineered sequences have remained limited in scale. Here, we use random sequences as an alternative, allowing us to measure the expression output of over 100 million synthetic yeast promoters. Random sequences yield a broad range of reproducible expression levels, indicating that the fortuitous binding sites in random DNA are functional. From these data we learn models of transcriptional regulation that predict over 94% of the expression driven from independent test data and nearly 89% from sequences from yeast promoters. These models allow us to characterize the activity of TFs and their interactions with chromatin, and help refine cis-regulatory motifs. We find that strand, position, and helical face preferences of TFs are widespread and depend on interactions with neighboring chromatin. Such massive-throughput regulatory assays of random DNA provide the diverse examples necessary to learn complex models of cis-regulatory logic.

genomics↗