Gideon Grafi

• Ben-Gurion University of the Negev

Our aim was to quantify the life‐history strategies of the cold desert annual species Alyssum linifolium and Tetracme quadricornis (Brassicaceae), with particular emphasis on the seed stage. Freshly matured seeds were tested for germination over a range of alternating temperature regimes in light and in dark, and the effects of seed coat scarificat...

Lunar farming, often regarded as a myth, is regularly practiced in many places around the world (e.g., India) where framers organized their agricultural activities according to moon phases. Early and recent work showed that exposure to moonlight affects the life cycle of plants, from seed germination and vegetative growth to fruit maturation and di...

The H2B.8 variant has been diverged from other variants by its extended N-terminal region that possesses a conserved domain. We generated transgenic Arabidopsis plants expressing H2B.9 (class I), H2B.5 (class II) and H2B.8 (class III) fused to GFP under the 35 S promoter and studied their nuclear distribution and function. H2B.8-GFP showed peculiar...

Agriculture-based industries generate huge amounts of byproducts/wastes every year, which are not exploited or disposed efficiently posing an environmental problem with implications to human and animal health. Finding strategies to increase the recycling of agro-industrial byproducts/wastes (AIBWs) is a primary objective of the current study. A tho...

Climate change is expected to increase the frequency and severity of abiotic stresses (e.g., hot spell, salinity, drought), which might lead to loss of crop yield. We investigated the effect of salinity (S), short episodes of high temperature (HS) and combination of S+HS at the reproductive phase on seeds and dead pericarps properties of the crop p...

Main conclusion A multi-year study of perennial Z. dumosum shows a consistent seasonal pattern in the changes of petiole metabolism, involving mainly organic acids, polyols, phenylpropanoids, sulfate conjugates, and piperazines. Abstract GC–MS and UPLC–QTOF-MS-based metabolite profiling was performed on the petioles of the perennial desert shrub Z...

Rhythmic exposure to moonlight has been shown to affect animal behavior, but its effects on plants, often observed in lunar agriculture, have been doubted and often regarded as myth. Consequently, lunar farming practices are not well scientifically supported, and the influence of this conspicuous environmental factor, the moon, on plant cell biolog...

Plants have two types of reproduction: sexual, resulting in embryo production, and asexual, resulting in vegetative bodies commonly derived from stems and roots (e.g., bulb, tuber). Dead organs enclosing embryos (DOEEs, such as seed coat and pericarp) are emerging as central components of the dispersal unit acting to nurture the embryo and ensure i...

Zygophyllum dumosum is a dominant shrub in the Negev Desert whose survival is accomplished by multiple mechanisms including abscission of leaflets to reduce whole plant transpiration while leaving the fleshy, wax-covered petioles alive but dormant during the dry season. Petioles that can survive for two full growing seasons maintain cell component...

The seed is the fundamental unit of the dispersal of dry, dehiscent fruits, in which the fruit splits open at maturity to allow for seed dispersal. However, dry fruits may be indehiscent and therefore represent the dispersal unit (DU). Cereals possess a one-seeded fruit, whereby the seed coat and the fruit coat are fused together to generate the ca...

In the face of climate change and the predicted increase in the frequency and severity of abiotic stresses (e.g., hot spell, salinity), we sought to investigate the effect of salinity (S), short episodes of high temperature (HS) and combination of salinity and high temperature (SHS), at the reproductive phase, on yield with a special focus on the p...

Dead organs enclosing embryos, such as seed coats and pericarps, are emerging as important maternally-derived components of the dispersal unit that affect seed performance and fate. In the face of climate change and increased incidents of heatwaves, we sought to investigate the effect of salinity (S), short episodes of high temperature (HS), and co...

Dry fruits consist of two types, dehiscent and indehiscent, whereby the fruit is splitting open or remains closed at maturity, respectively. The seed, the dispersal unit (DU) of dehiscent fruits, is composed of three major parts, the embryo and the food reserve, encapsulated by the maternally-derived organ, the seed coat. Indehiscent fruit constitu...

Besides chemical modification of histone proteins, chromatin dynamics can be modulated by histone variants. Most organisms possess multiple genes encoding for core histone proteins, which are highly similar in amino acid sequence. The Arabidopsis thaliana genome contains 11 genes encoding for histone H2B (HTBs), 13 for H2A (HTAs), 15 for H3 (HTRs),...

Main conclusion The dead husk is a vital component of the dispersal unit whose biochemical properties can be modified following exposure to drought. This might affect seed performance and fate, soil properties and consequently plant biodiversity. Abstract We investigated the effects of extreme drought on the dispersal unit (DU) properties of winte...

The dead organs enclosing embryos (DOEEs) emerge as central components of the dispersal unit (DU) capable for long-term storage of active proteins and other substances that affect seed performance and fate. We studied the effect of maternal environment (salt and salt+heat) on progeny DU (dry indehiscent fruit) focusing on pericarp properties of Ana...

Understanding ecosystem response to drier climates calls for modeling the dynamics of dryland plant populations, which are crucial determinants of ecosystem function, as they constitute the basal level of whole food webs. Two modeling approaches are widely used in population dynamics, individual (agent)-based models and continuum partial-differenti...

Highlights Sex-determination in Mercurialis annua is not related to chromatin conformation or DNA methylation of floral homeotic genes but might be regulated through upstream of these genes by an unknown gender-specific factor(s) that affects hormonal-homeostasis. Abstract In plants, dioecy characterizes species carrying male and female flowers on...

Plants thriving in harsh desert environments provide a suitable bio-system for unraveling novel mechanisms for survival under seasonal climate change and combination of temperature extremes, low water and nutrient availability and high salinity and radiation levels. The study of the desert plant Zygophyllum dumosum Boiss in its the natural habitat...

The biochemical composition of Zygophyllum dumosum Boiss (Zygophyllaceae) was analyzed in petioles collected in the summer and winter from plants growing in a natural ecosystem on a southeast-facing slope of the Negev desert. UPLC-QTOF MS based analysis identified season specific sulfur containing phenylpropanoids unreported in plants. Sulfuric-caf...

In plants, dioecy characterizes species carrying male and female flowers on separate plants and occurs in about 6% of angiosperms. To date, the molecular mechanism(s) underlying sexual dimorphism is essentially unknown. The ability of gender-reversal by hormone application suggests that epigenetics might play an important role in sexual dimorphism....

Abstract Background CHROMOMEHYLASE1 (CMT1) has long been considered a non-essential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the retroelement Evelknievel (EK),inserted within exon 13,or contains frame-shift mutations resulting in a truncated, non-functional protein. Here, we wanted to explore the regulatory pathw...

Background The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein. In contrast to other transposable elements, no tr...

Plants have evolved a variety of dispersal units whereby the embryo is enclosed by various dead protective layers derived from maternal organs of the reproductive system including seed coats (integuments), pericarps (ovary wall, e.g., indehiscent dry fruits) as well as floral bracts (e.g., glumes) in grasses. Commonly, dead organs enclosing embryos...

Plants have evolved a variety of dispersal units whereby the embryo is enclosed by various dead protective layers derived from maternal organs of the reproductive system including seed coats (integuments), pericarps (ovary wall, e.g., indehiscent dry fruits) as well as floral bracts (e.g. glumes) in grasses. Commonly, dead organs enclosing embryos...

Plants thriving in desert environments are suitable for studying mechanisms for plant survival under extreme seasonal climate variation. We studied epigenetic mechanisms underlying seasonal growth cycles in the desert plant Zygophyllum dumosum Boiss., which was previously shown to be deficient in repressive markers of di-methyl and tri-methyl H3K9...

Plants thriving in desert environments are suitable for studying mechanisms for plant survival under extreme seasonal climate variation. Zygophyllum dumosum Boiss, like many other Zygophyllaceae species, displays a unique epigenetic mechanism whereby the repressive markers di- and tri-methyl of H3K9 do not exist. We studied epigenetic mechanisms un...

Results: Methylome databases confirmed that EK retroelement is heavily methylated but methylation is extended toward CMT1 downstream region. Strong transcriptional activation of EK accompanied by significant reduction in non-CG methylation was found in cmt3 and kyp2, but not in ddm1 or RdDM mutants. EK activation in cmt3 and kyp2 did not interfere...

Objectives: It is a common practice in Arabidopsis to transfer a mutation generated in one genetic background to other genetic background via crossing. However, the drawback of this methodology is unavoidable presence of genomic fragments from the donor parent being often replacing desirable genomic fragments of the recurrent parent. Here, we high...

It is commonly assumed that dead pericarps of dry indehiscent fruits have evolved to provide an additional physical layer for embryo protection and as a means for long distance dispersal. The pericarps of dry fruits undergo programmed cell death (PCD) during maturation whereby most macromolecules such DNA, RNA, and proteins are thought to be degrad...

Seed development culminates in programmed cell death (PCD) and hardening of organs enclosing the embryo (e.g., pericarp, seed coat) providing essentially a physical shield for protection during storage in the soil. We examined the proposal that dead organs enclosing embryos are unique entities that store and release upon hydration active proteins t...

Figure A. Functional classification of released proteins from Arabidopsis (Col) seeds. Figure B. Timing of release of nucleases from the S. alba seeds following hydration. Figure C. Nuclease activities released from seed coats of various leguminous plants. S1 Table. A list of plant species used in the present study. S2 Table. Proteome parameter def...

It is commonly assumed that the dead, hardened floral bracts of the dispersal unit of grasses have been evolved to protect seeds from predation and / or assist in fruit/caryopsis dispersal. While these structures have important agronomical and economical implications, their adaptive value has not been fully explored. We investigated the hypothesis...

Data set 1. Proteome raw data of all proteins released from dead glumes of wild emmer wheat. (XLSX)

Data set 2. List of proteins released from dead glumes of wild emmer wheat after filtering. (XLSX)

Raviv et al. submitted manuscript. (PDF)

Data set 3. GO term classification. (XLSX)

Proteome parameter definition. (PDF)

Cell dedifferentiation characterizes the transition of leaf cells to protoplasts and is accompanied by global chromatin decondensation. Here we show that in Arabidopsis, chromocentric chromatin undergoes prompt and gradual decondensation upon protoplasting. We hypothesized that prompt chromatin decondensation is unlikely to be driven solely by epig...

Expression of the Arabidopsis endonuclease encoding genes in various tissues and following exposure to stress. (DOCX)

Senescence represents the final stage of leaf development but is often induced prematurely following exposure to biotic and abiotic stresses. Leaf senescence is manifested by color change from green to yellow (due to chlorophyll degradation) or to red (due to de novo synthesis of anthocyanins coupled with chlorophyll degradation) and frequently cul...

Leaves of cereal plants display nucleosomal fragmentation of DNA attributed to the action of nucleases induced during program cell death (PCD). Yet, the specific nuclease activity responsible for generating double strand DNA breaks (DSBs) that lead to DNA fragmentation has not been fully described. Here, we characterized a Ca(++)/Mg(++)-dependent S...

Harvester ants are common and very efficient granivores in many regions of the world. The ants may collect dispersed seeds from the ground or climb on plants to harvest seeds. While collecting or harvesting wild cereal seeds they first trim the long and bulky awns to allow better seed transportation to their nests and through the narrow passages in...

The desert plant Zygophyllum dumosum displays unique epigenetic constraints, not found in other perennial desert plants, namely, it possesses mono- but not di- and tri-methylated histone H3 at lysine 9 (H3K9). We investigated the proposal that lack of dimethylated H3K9 (H3K9me2) is not restricted to Z. dumosum, but a feature uniquely evolved in the...

Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress,...

DEAD-box RNA helicases are involved in many aspects of RNA metabolism and in diverse biological processes in plants. Arabidopsis thaliana mutants of two DEAD-box RNA helicases, STRESS RESPONSE SUPPRESSOR1 (STRS1) and STRS2 were previously shown to exhibit tolerance to abiotic stresses and up-regulated stress-responsive gene expression. Here, we sho...

Background: Previous data suggested that senescing cells or cells exposed to acute stress may acquire stem cell properties characterized by open chromatin conformation and by promiscuous expression of transcription factor genes. To further explore the link between stress response and dedifferentiation, we generated transgenic plants in which a rep...

Stem cells have become a major topic, both publicly and scientifically, owing to their potential to cure diseases and repair damaged tissues. Particular attention has been given to the so-called "induced pluripotent stem cells" (iPSCs) in which somatic cells are induced by the expression of transcription factor encoding transgenes-a methodology fir...

The chemical marks that provide the major means by which epigenetics manifests its effect on chromatin structure and function have been discovered long ago almost along with the invention of the term epigenome by Conrad H. Waddington. However, it had to wait several decades before the connection between epigenetics and chemical modifications of DNA...

Seeds in the seed bank experience diurnal cycles of imbibition followed by complete dehydration. These conditions pose a challenge to the regulation of germination. The effect of recurring hydration-dehydration (Hy-Dh) cycles were tested on seeds from four Arabidopsis thaliana accessions [Col-0, Cvi, C24 and Ler]. Diurnal Hy-Dh cycles had a detrime...

Stem cells are commonly defined by their developmental capabilities, namely, self-renewal and multitype differentiation, yet the biology of stem cells and their inherent features both in plants and animals are only beginning to be elucidated. In this review article we highlight the stem cell state in plants with reference to animals and the plastic...

Plant response to various stress conditions often results in expression of common genes, known as stress-responsive/inducible genes. Accumulating data point to a common, yet elusive process underlying the response of plant cells to stress. Evidence derived from transcriptome profiling of shoot apical meristem stem cells, dedifferentiating protoplas...

Dedifferentiation signifies the capacity of somatic cells to acquire stem cell-like properties. This process can be induced during normal development and as a response to various stimuli, such as pathogen infection and wounding. Dedifferentiation also characterizes the transition of differentiated leaf cells into protoplasts (plant cells devoid of...

Zygophyllum dumosum Boiss. is a perennial Saharo-Arabian phytogeographical element and a dominant shrub on the rocky limestone southeast-facing slopes of the Negev desert. The plant is highly active during the winter, and semideciduous during the dry summer, i.e., it sheds its leaflets, while leaving the thick, fleshy petiole green and rather activ...

The high mobility group (HMG) proteins are nonhistone chromosomal proteins that participate in diverse nuclear activities including chromatin structure and gene regulation. We previously studied the biochemistry of the maize HMGA protein and its role in transcriptional regulation during maize endosperm development. Here, we extended our study and s...

The Arabidopsis MBD7 (AtMBD7) - a naturally occurring poly MBD protein - was previously found to be functional in binding methylated-CpG dinucleotides in vitro and localized to highly methylated chromocenters in vivo. Furthermore, AtMBD7 has significantly lower mobility within the nucleus conferred by cooperative activity of its three MBD motifs. H...

Cellular dedifferentiation underlies topical issues in biology, such as regeneration and somatic cell nuclear transfer (SCNT), and signifies the withdrawal of cells from a given differentiated state into a 'stem cell'-like state that confers pluripotency. Recently, there has been growing interest in exploiting the dedifferentiation process to obtai...

Serine 10 phosphorylation of histone H3 (H3S10ph) has long been considered a mitotic marker, which is often associated with chromosome condensation both in plants and animals. Yet, in animal cells, H3S10ph was found associated with transcriptional activation of genes. Here we extend this view to plant cells showing that H3S10ph not only occurs in d...

Three methyl-CpG-binding domain (MBD) proteins in Arabidopsis, AtMBD5, AtMBD6, and AtMBD7, are functional in binding methylated CpG dinucleotides in vitro and localize to the highly CpG-methylated chromocenters in vivo. These proteins differ, however, in their subnuclear localization pattern; AtMBD5 and AtMBD6, each containing a single MBD motif, s...

SummaryA probe made from a recombinant human β-interferon DNA detected specific bands in Southern blots of restriction enzyme-cleaved tobacco DNA. Specific tobacco DNA fragments also hybridized with a similar probe made from a clone of human 2′,5′-linked oligoadenylate (2–5A) synthetase. The expression of these plant genes was analysed by Northern...

Cellular dedifferentiation underlies topical issues in biology such as regeneration and nuclear cloning and has common features in plants and animals. In plants, this process characterizes the transition of differentiated leaf cells to protoplasts (plant cells devoid of cell walls) and is accompanied by global chromatin reorganization associated wi...

Cytosine methylation is the most prevalent epigenetic modification of plant nuclear DNA, which occurs in symmetrical CpG or CpNpG as well as in non-symmetrical contexts. Intensive studies demonstrated the central role played by cytosine methylation in genome organization, gene expression and in plant growth and development. However, the way by whic...

The effect of DNA methylation on various aspects of plant cellular and developmental processes has been well documented over the past 35 years. However, the underlying molecular mechanism interpreting the methylation signal has only recently been explored with the isolation and characterization of the Arabidopsis methyl-CpG-binding domain (MBD) pro...

Final fruit size in pear depends on the combined contributions of the number of cells present at fruit-set, the number of subsequent cell divisions, and on cell expansion. To date, in spite of the commercial application of cytokinins to induce larger fruits, no detailed studies have addressed the question of how cytokinin signalling and cell divisi...

Plants possess a single gene for the structurally related HETEROCHROMATIN PROTEIN1 (HP1), termed LIKE-HP1 (LHP1). We investigated the subnuclear localization, binding properties, and dynamics of LHP1 proteins in Arabidopsis thaliana cells. Transient expression assays showed that tomato (Solanum lycopersicum) LHP1 fused to green fluorescent protein...

Methyl-CpG binding domain (MBD) proteins in Arabidopsis thaliana bind in vitro methylated CpG sites. Here, we aimed to characterize the binding properties of AtMBDs to chromatin in Arabidopsis nuclei. By expressing in wild-type cells AtMBDs fused to green fluorescent protein (GFP), we showed that AtMBD7 was evenly distributed at all chromocenters,...

The basic relationships between cytokinin signaling, cell division and fruit growth are well established. Final fruit size depends on the combined effects of the number of cells present at fruit set, the number of subsequent cell divisions, and the extent of cell expansion. Most studies related to the cell cycle in developing fruits have been perfo...

To compensate for the lack of chilling requirements of fruit trees grown in relatively hot climate, chemical treatments to break bud dormancy have to be applied. The success of such treatments depends on the identification of the proper stage of dormancy development. To date, no reliable means exists to indicate bud developmental stages in the orch...

Post-translational modifications of core histone proteins play a key role in chromatin structure and function. Here, we study histone post-translational modifications during reentry of protoplasts derived from tobacco mesophyll cells into the cell cycle and evaluate their significance for progression through mitosis. Methylation of histone H3 at ly...

Inactivation of the Arabidopsis protein FERTILIZATION INDEPENDENT ENDOSPERM (FIE) induces division of the central cell of the embryo sac, leading to endosperm development in the absence of fertilization. The mechanism whereby FIE regulates this process is unknown. We postulated that activation of central cell division in fie mutant plants might inv...

Cells in maize (Zea mays) endosperm undergo multiple cycles of endoreduplication, with some attaining DNA contents as high as 96C and 192C. Genome amplification begins around 10 d after pollination, coincident with cell enlargement and the onset of starch and storage protein accumulation. Although the role of endoreduplication is unclear, it is tho...

The transition from leaf cells to protoplasts (plant cells devoid of cell walls) confers pluripotentiality coupled with chromatin reorganization. Here, we sought to identify remodeled chromosomal domains in Arabidopsis protoplasts by tracking DNA sequences undergoing changes in DNA methylation and by identifying up-regulated genes. We observed a re...

The remarkable regenerative capacity displayed by plants and various vertebrates, such as amphibians, is largely based on the capability of somatic cells to undergo dedifferentiation. In this process, mature cells reverse their state of differentiation and acquire pluripotentiality--a process preceding not only reentry into the cell cycle but also...

The remarkable regeneration capacity of plant cells is based on their capability to dedifferentiate. We recently reported that cellular dedifferentiation proceeds through two distinct phases, each accompanied by chromatin decondensation: acquisition of competence for fate switch followed by a signal-dependent reentry into S phase. The purpose of th...

Cytosine methylation at symmetrical CpG and CpNpG sequences plays a key role in the epigenetic control of plant growth and development; yet, the way by which the methylation signal is interpreted into a functional state has not been elucidated. In animals, the methylation signal is recognized by methyl-CpG-binding domain (MBD) proteins that specifi...

Heterochromatin protein 1 (HP1) controls heterochromatin formation in animal cells, at least partly through interaction with lysine 9 (Lys-9)-methylated histone H3. We aimed to determine whether a structurally conserved human HP1 protein exhibits conserved heterochromatin localization in plant cells and studied its relation to modified histone H3....

On Jun 1, 2005 this sequence version replaced gi:16519032.

Cellular dedifferentiation is the major process underlying totipotency, regeneration, and formation of new stem cell lineages in multicellular organisms. In animals it is often associated with carcinogenesis. Here, we used tobacco protoplasts (plant cells devoid of cell wall) to study changes in chromatin structure in the course of dedifferentiatio...

Class I knox genes play an important role in shoot meristem function and are thus involved in the ordered development of stems, leaves, and reproductive organs. To elucidate the mechanism underlying the expression pattern of these homeobox genes, we studied a spontaneous tomato (Lycopersicon esculentum) mutant that phenotypically resembles, though...

During maize endosperm development, cells shift from a mitotic cycle to endoreduplication, driving the massive synthesis of storage proteins (zeins) and starch. In this developmental context, we studied changes in expression levels of histone H1 and high mobility group I/Y (HMG-I/Y), two chromatin architectural proteins that are known to affect gen...

During maize endosperm development, cells shift from a mitotic cycle to endoreduplication, driving the massive synthesis of storage proteins (zeins) and starch. In this developmental context, we studied changes in expression levels of histone H1 and high mobility group I/Y (HMG-I/Y), two chromatin architectural proteins that are known to affect gen...

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In recent years considerable effort has been invested toward understanding the molecular mechanisms that regulate and restrict DNA replication to once per each cell cycle. An important contribution came from studying the phenomenon of endoreduplication-an endonuclear duplication of chromosomes which occurs in the absence of mitosis leading to the p...

Retinoblastoma (RB-1) is a tumor suppressor gene that encodes a 105-kDa nuclear phosphoprotein. To date, RB genes have been isolated only from metazoans. We have isolated a cDNA from maize endosperm whose predicted protein product (ZmRb) shows homology to the "pocket" A and B domains of the Rb protein family. We found ZmRb behaves as a pocket prote...

On Jan 30, 2002 this sequence version replaced gi:1277179.