Biology subjects

Shapira, O.

Publications and source records attributed to Shapira, O..

10 recordsLinked to original sources

bioRxiv2026

Stem photosynthesis from wild Prunus arabica enhances growth, advances bloom and increases yield in cultivated almond

Rising winter temperatures threaten deciduous fruit tree productivity by depleting carbohydrate reserves during dormancy. This study investigated Stem Photosynthetic Capacity (SPC), a rare adaptive trait from wild Prunus arabica, as a mechanism to enhance almond carbon economy. Using extreme segregating groups from the F1 population (P. dulcis X P. arabica), we evaluated physiological performance through high-resolution lysimetric and multi-year orchard monitoring. High-SPC [SPC(+)] genotypes maintained significantly greater stem CO2 assimilation and transpiration during leafless periods compared to low-SPC [SPC(-)] progenies. Over five successive seasons, SPC(+) trees exhibited a 33.3% increase in trunk secondary growth and reached 10% bloom approximately 8 days earlier. Most importantly, the SPC(+) group achieved a 4.6-fold increase in mean kernel yield when compared to SPC(-) group. These findings demonstrate that SPC provides a flexible, supplementary winter carbon source that directly supports both vegetative and reproductive development. Integrating SPC into commercial almond breeding programs may offer a valuable strategy to improve climate resilience and help sustain yields under warming conditions. HighlightIntegrating stem photosynthesis into commercial almond hybrids provides a winter carbon source that advances blooming, expands trunk growth by [~]33%, and increases kernel yields by more than 4.5-fold.

Plant Biology↗

bioRxiv2026

Ethylene biosynthesis in guard cells, not mesophyll, predominantly drives stomatal conductance responses to CO2

O_LIResearch and rationale: This study investigates whether tissue-specific ethylene biosynthesis regulates stomatal conductance (gs) responses to changing [CO2] in Arabidopsis thaliana. While guard cells sense [CO2], mesophyll-derived signals are also implicated in stomatal control. We aimed to determine if ethylene production in guardcells or mesophyll is the primary driver of CO2-induced gs regulation. C_LIO_LIMethods: An acs octuple mutant with severely reduced ethylene production was complemented with tissue-specific ACS8/ACS11 transgenes driven by guard-cell, spongy-mesophyll, dual palisade/spongy-mesophyll, or whole-leaf promoters. Tissue-specific complementation in the different transgenic lines was confirmed and evaluated by qPCR, tissue-specific NEON expression, microscopic imaging, and ethylene production measurements. Gas-exchange measurements on intact plants recorded gs kinetics, CO2 assimilation, and water-use efficiency, across CO2 shifts. C_LIO_LIKey results: Guard-cell complementation nearly fully restored wild-type gs responses and reversed the mutants aberrant leaf phenotype. Spongy-mesophyll complementation failed to rescue either trait, while dual palisade- and spongy-mesophyll complementation yielded only partial recovery. C_LIO_LIConclusion: Ethylene produced in guard cells is the dominant regulator of CO2-induced stomatal conductance regulation, with mesophyll-derived ethylene contributing secondarily via long-distance signaling or by augmenting the overall ethylene pool. These findings underscore the importance of spatially regulated ethylene biosynthesis in balancing carbon assimilation and transpiration. C_LI

plant biology↗

bioRxiv2025

Disentangling the stomatal response to transpiration and relative humidity

Stomatal responses to atmospheric conditions are critical for balancing plant CO2 gain with water loss. Yet, the question of whether stomata respond directly to humidity or to the rate of water loss (transpiration) remains unresolved due to the tight coupling between these variables. To decouple them, we manipulated water vapor diffusivity using Helox (21% O2, 79% He), where vapor diffuses 2.33 times faster than in air, and Argox (21% O2, 79% Ar), where it diffuses 0.75 times slower. This allows control of VPD and transpiration independent of one another while maintaining a constant leaf temperature. We investigated the stomatal conductance (gsw) responses to air and Helox in several plant species, including Solanum lycopersicum, Vitis vinifera, and the fern Nephrolepis exaltata. In addition, we tested the Commelina communis, with coupled gas exchange and real-time imaging of stomatal aperture in intact leaves. In all angiosperms tested, we observed that stomatal closing was triggered exclusively by reductions in RH rather than by transpiration increases. When transpiration increased, but relative humidity remained constant, we detected an increase in gsw without a following decrease in the experimental time span. Exposure to Argox without altering RH reduced transpiration, likely enabling restoration of epidermal turgor and inducing passive mechanical closure. However, the rate of stomatal closure under reduced RH was 2.35 times faster than that observed under Argox, suggesting that passive turgor-driven responses cannot fully explain the kinetics or extent of closure under dry air. This work provides direct experimental evidence for humidity-driven stomatal closure.

plant biology↗

bioRxiv2024

Recurrent breakpoints in the BRD4 locus reduce toxicity associated with gene amplification

Structural variants (SVs) represent a mechanism by which cancer cells activate oncogenes or disrupt the function of genes with tumor suppressor roles. A recent study by the PCAWG Consortium investigated structural variants in 30 tumor types, identifying focal rearrangements in the oncogenic BRD4 gene in ovarian, endometrial and breast cancers. These rearrangements resulted in decreased BRD4 expression despite increased copy number, suggesting a novel mechanism to finetune gene over-expression. In this study, we show that focal deletions of BRD4 disrupt genomic regulatory regions and impact gene isoform expression in breast and ovarian tumors when compared to their expression across normal tissues. To determine the functional impact of these concomitant amplification and focal deletion events, we first leveraged open-reading-frame (ORF) screen data from 16 cancer cell lines, where we observed that overexpression of BRD4-long and BRD4-short isoforms is toxic for cancer cell growth. We confirmed these results in OVSAHO ovarian cancer cells, where overexpression of both isoforms significantly reduced tumor growth. Next, we mimicked the focal deletions occurring in BRD4 regulatory regions by CRISPR-Cas9 technology, and observed that their depletion functionally ablates tumor cell growth. We finally show that these focal deletions rescue ovarian carcinoma cells from the toxicity effects associated with gene overexpression, suggesting that global BRD4 gene expression levels must be fine tuned to ensure proper cancer cell proliferation. Our study provides experimental evidence for BRD4 deletions constituting the first example of a driver SV alteration reducing toxicity in cancer, therefore expanding the landscape of cancer progression mechanisms.

cancer biology↗

bioRxiv2023

Wind speed affects the rate and kinetics of stomatal conductance

Understanding the relationship between wind speed and gas exchange in plants is a longstanding challenge. Our aim was to investigate the impact of wind speed on maximum rates of gas exchange and the kinetics of stomatal responses. We conducted experiments using an infrared gas analyzer equipped with a controlled leaf fan, enabling precise control of the boundary layer conductance. We first showed that the chamber was adequately mixed even at extremely low fan speeds (down to 200 rpm, equivalent to a wind speed of 0.0005 m s-1) and evaluated the link between fan speed, wind speed, and boundary layer conductance. We observed that higher wind speeds led to increased gas exchange of both water vapor and CO2 in Arabidopsis, presumably due to its effect on transpiration and the consequential reduction in epidermal pressure that led to stomatal opening. We documented that stomatal opening in response to light was three times faster at a fan speed of 10000 rpm (wind speed of 2 m s-1) compared with 500 rpm (0.25 m s-1) in Vicia faba, while the latter exhibited an opening rate that was similar to those of epidermal peels. The increase of stomatal conductance under high wind was observed in four species under field conditions. Our findings demonstrate the importance of the size of the boundary layer on determining maximum rates of gas exchange and the kinetics of gas exchange responses to environmental changes.

plant biology↗

bioRxiv2023

Detecting significantly recurrent genomic connections from simple and complex rearrangements in the cancer genome

The detection of somatic genetic alterations that recur across cancer genomes more than expected by chance has been a major goal of cancer genomics, as these alterations are enriched for "driver" events that promote cancer. Multiple methods have been developed to detect driver point mutations and copy-number variants, but methods to detect driver rearrangements have largely not been pursued. Unlike point mutations and copy-number alterations, which can be assigned to a single genomic locus, rearrangements connect two distant genomic loci, and possibly more in the case of complex or clustered events. Here, we explore genomic features that predict the rate at which any pair of loci will be connected by rearrangements and describe two methods to detect rearrangements that recur more often than this background rate. The first, SVSig-2D, detects pairs of loci that are directly connected by a single rearrangement; the second, SVSig-2Dc also detects loci that are recurrently connected indirectly through two or more rearrangements. When applied to a pan-cancer dataset of over 2,500 cancers, these methods identified 80 significantly recurrent simple rearrangements and 29 complex rearrangements, including both known and novel events. Intriguingly, though both recurrent simple and complex rearrangements tended to be tissue-specific, this was less true for the complex events. The detection of recurrent rearrangements with methods such as these will be an essential component of cancer genomics in the whole-genome sequencing era.

genomics↗

bioRxiv2021

Nitrogen uptake and macronutrients distribution in mango trees (cv. Keitt) under three N fertigation treatments

We assessed the effects of N concentration in the irrigation water on nutrient uptake and distribution in leaves and fruit of mango cv. Keitt grown in a lysimeter for four years. We applied three treatments: N1 - no N fertilization (less than 2 mg/L in the tap water); N2 - 10 mg/L N; N3 - 20 mg/L N. Deficient N conditions (N1) generated low vegetative yield, high fruit:leaf ratio, high photosynthetic activity, high leaf P and K concentrations, and high sugar content along with low acidity in the fruit. Excess N concentration (N3) induced vegetative growth, and reduced fruit yield and gas-exchange characteristics. The calculated annual nitrogen uptake heavily depended on the nitrogen supply (N1-26 g/tree; N2-196 g/tree; N3- 185 g/tree). Fruits were the major N sink being 0.82, 0.26 and 0.05 from the total annual N supplied. The N quantities accumulated in N1 fruits during the reproductive season (May-August), were above the N quantities supplied via fertigation, suggesting that N reserve in the vegetative tissues supplied the fruits high N demand. The finding shows the importance of adequate nitrogen supply to mango trees and the dangers of excessive fertilization.

physiology↗

bioRxiv2017

The whole-genome panorama of cancer drivers

The advance of personalized cancer medicine requires the accurate identification of the mutations driving each patients tumor. However, to date, we have only been able to obtain partial insights into the contribution of genomic events to tumor development. Here, we design a comprehensive approach to identify the driver mutations in each patients tumor and obtain a whole-genome panorama of driver events across more than 2,500 tumors from 37 types of cancer. This panorama includes coding and non-coding point mutations, copy number alterations and other genomic rearrangements of somatic origin, and potentially predisposing germline variants. We demonstrate that genomic events are at the root of virtually all tumors, with each carrying on average 4.6 driver events. Most individual tumors harbor a unique combination of drivers, and we uncover the most frequent co-occurring driver events. Half of all cancer genes are affected by several types of driver mutations. In summary, the panorama described here provides answers to fundamental questions in cancer genomics and bridges the gap between cancer genomics and personalized cancer medicine.

cancer biology↗

bioRxiv2017

Selective and mechanistic sources of recurrent rearrangements across the cancer genome

Cancer cells can acquire profound alterations to the structure of their genomes, including rearrangements that fuse distant DNA breakpoints. We analyze the distribution of somatic rearrangements across the cancer genome, using whole-genome sequencing data from 2,693 tumor-normal pairs. We observe substantial variation in the density of rearrangement breakpoints, with enrichment in open chromatin and sites with high densities of repetitive elements. After accounting for these patterns, we identify significantly recurrent breakpoints (SRBs) at 52 loci, including novel SRBs near BRD4 and AKR1C3. Taking into account both loci fused by a rearrangement, we observe different signatures resembling either single breaks followed by strand invasion or two separate breaks that become joined. Accounting for these signatures, we identify 90 pairs of loci that are significantly recurrently juxtaposed (SRJs). SRJs are primarily tumor-type specific and tend to involve genes with tissue-specific expression. SRJs were frequently associated with disruption of topology-associated domains, juxtaposition of enhancer elements, and increased expression of neighboring genes. Lastly, we find that the power to detect SRJs decreases for short rearrangements, and that reliable detection of all driver SRJs will require whole-genome sequencing data from an order of magnitude more cancer samples than currently available.

cancer biology↗

bioRxiv2017

Patterns of structural variation in human cancer

A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments ranging in size from kilobases to whole chromosomes. We developed methods to group, classify and describe structural variants, applied to >2,500 cancer genomes. Nine signatures of structural variation emerged. Deletions have trimodal size distribution; assort unevenly across tumour types and patients; enrich in late-replicating regions; and correlate with inversions. Tandem duplications also have trimodal size distribution, but enrich in early-replicating regions, as do unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy number gains and frequent inverted rearrangements. One prominent structure consists of 1-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, frequently activating the telomerase gene, TERT, in liver cancer. Cancers access many rearrangement processes, flexibly sculpting the genome to maximise oncogenic potential.

cancer biology↗