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11.4: Plant Responses to Light - Biology

11.4: Plant Responses to Light - Biology



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Plants have a number of sophisticated uses for light that go far beyond their ability to photosynthesize low-molecular-weight sugars using only carbon dioxide, light, and water. Photomorphogenesis is the growth and development of plants in response to light. Photoperiodism is the ability to use light to track time. Phototropism is a directional response that allows plants to grow towards, or even away from, light.

The sensing of light in the environment is important to plants; it can be crucial for competition and survival. The response of plants to light is mediated by different photoreceptors, which are comprised of a protein covalently bonded to a light-absorbing pigment called a chromophore. Together, the two are called a chromoprotein.

The red/far-red and violet-blue regions of the visible light spectrum trigger structural development in plants. Sensory photoreceptors absorb light in these particular regions of the visible light spectrum because of the quality of light available in the daylight spectrum. In terrestrial habitats, light absorption by chlorophylls peaks in the blue and red regions of the spectrum. As light filters through the canopy and the blue and red wavelengths are absorbed, the spectrum shifts to the far-red end, shifting the plant community to those plants better adapted to respond to far-red light. Blue-light receptors allow plants to gauge the direction and abundance of sunlight, which is rich in blue–green emissions. Water absorbs red light, which makes the detection of blue light essential for algae and aquatic plants.

The Phytochrome System and the Red/Far-Red Response

The phytochromes are a family of chromoproteins with a linear tetrapyrrole chromophore, similar to the ringed tetrapyrrole light-absorbing head group of chlorophyll. Phytochromes have two photo-interconvertible forms: Pr and Pfr. Pr absorbs red light (~667 nm) and is immediately converted to Pfr. Pfr absorbs far-red light (~730 nm) and is quickly converted back to Pr. The minute difference between light defined as red or far-red is very important in this reaction. Absorption of red or far-red light causes a massive change to the shape of the chromophore, altering the conformation and activity of the phytochrome protein to which it is bound. Pfr is the physiologically active form of the protein; therefore, exposure to red light yields physiological activity. Exposure to far-red light inhibits phytochrome activity. Together, the two forms represent the phytochrome system (Figure 1).

The phytochrome system acts as a biological light switch. It monitors the level, intensity, duration, and color of environmental light. The effect of red light is reversible by immediately shining far-red light on the sample, which converts the chromoprotein to the inactive Pr form. Additionally, Pfr can slowly revert to Pr in the dark, or break down over time. In all instances, the physiological response induced by red light is reversed. The active form of phytochrome (Pfr) can directly activate other molecules in the cytoplasm, or it can be trafficked to the nucleus, where it directly activates or represses specific gene expression.

Once the phytochrome system evolved, plants adapted it to serve a variety of needs. Unfiltered, full sunlight contains much more red light than far-red light. Because chlorophyll absorbs strongly in the red region of the visible spectrum, but not in the far-red region, any plant in the shade of another plant on the forest floor will be exposed to red-depleted, far-red-enriched light. The preponderance of far-red light converts phytochrome in the shaded leaves to the Pr (inactive) form, slowing growth. The nearest non-shaded (or even less-shaded) areas on the forest floor have more red light; leaves exposed to these areas sense the red light, which activates the Pfr form and induces growth. In short, plant shoots use the phytochrome system to grow away from shade and towards light. Because competition for light is so fierce in a dense plant community, the evolutionary advantages of the phytochrome system are obvious.

In seeds, the phytochrome system is not used to determine direction and quality of light (shaded versus unshaded). Instead, is it used merely to determine if there is any light at all. This is especially important in species with very small seeds, such as lettuce. Because of their size, lettuce seeds have few food reserves. Their seedlings cannot grow for long before they run out of fuel. If they germinated even a centimeter under the soil surface, the seedling would never make it into the sunlight and would die. In the dark, phytochrome is in the Pr (inactive form) and the seed will not germinate; it will only germinate if exposed to light at the surface of the soil. Upon exposure to light, Pr is converted to Pfr and germination proceeds.

Plants also use the phytochrome system to sense the change of season. Photoperiodism is a biological response to the timing and duration of day and night. It controls flowering, setting of winter buds, and vegetative growth. Detection of seasonal changes is crucial to plant survival. Although temperature and light intensity influence plant growth, they are not reliable indicators of season because they may vary from one year to the next. Day length is a better indicator of the time of year.

As stated above, unfiltered sunlight is rich in red light but deficient in far-red light. Therefore, at dawn, all the phytochrome molecules in a leaf quickly convert to the active Pfr form, and remain in that form until sunset. In the dark, the Pfr form takes hours to slowly revert back to the Pr form. If the night is long (as in winter), all of the Pfr form reverts. If the night is short (as in summer), a considerable amount of Pfr may remain at sunrise. By sensing the Pr/Pfr ratio at dawn, a plant can determine the length of the day/night cycle. In addition, leaves retain that information for several days, allowing a comparison between the length of the previous night and the preceding several nights. Shorter nights indicate springtime to the plant; when the nights become longer, autumn is approaching. This information, along with sensing temperature and water availability, allows plants to determine the time of the year and adjust their physiology accordingly. Short-day (long-night) plants use this information to flower in the late summer and early fall, when nights exceed a critical length (often eight or fewer hours). Long-day (short-night) plants flower during the spring, when darkness is less than a critical length (often eight to 15 hours). Not all plants use the phytochrome system in this way. Flowering in day-neutral plants is not regulated by day length.

Try It

The word “horticulturist” comes from the Latin words for garden (hortus) and culture (cultura). This career has been revolutionized by progress made in the understanding of plant responses to environmental stimuli. Growers of crops, fruit, vegetables, and flowers were previously constrained by having to time their sowing and harvesting according to the season. Now, horticulturists can manipulate plants to increase leaf, flower, or fruit production by understanding how environmental factors affect plant growth and development.

Greenhouse management is an essential component of a horticulturist’s education. To lengthen the night, plants are covered with a blackout shade cloth. Long-day plants are irradiated with red light in winter to promote early flowering. For example, fluorescent (cool white) light high in blue wavelengths encourages leafy growth and is excellent for starting seedlings. Incandescent lamps (standard light bulbs) are rich in red light, and promote flowering in some plants. The timing of fruit ripening can be increased or delayed by applying plant hormones. Recently, considerable progress has been made in the development of plant breeds that are suited to different climates and resistant to pests and transportation damage. Both crop yield and quality have increased as a result of practical applications of the knowledge of plant responses to external stimuli and hormones.

Horticulturists find employment in private and governmental laboratories, greenhouses, botanical gardens, and in the production or research fields. They improve crops by applying their knowledge of genetics and plant physiology. To prepare for a horticulture career, students take classes in botany, plant physiology, plant pathology, landscape design, and plant breeding. To complement these traditional courses, horticulture majors add studies in economics, business, computer science, and communications.

The Blue Light Responses

Phototropism—the directional bending of a plant toward or away from a light source—is a response to blue wavelengths of light. Positive phototropism is growth towards a light source (Figure 2), while negative phototropism (also called skototropism) is growth away from light.

The aptly-named phototropins are protein-based receptors responsible for mediating the phototropic response. Like all plant photoreceptors, phototropins consist of a protein portion and a light-absorbing portion, called the chromophore. In phototropins, the chromophore is a covalently-bound molecule of flavin; hence, phototropins belong to a class of proteins called flavoproteins.

Other responses under the control of phototropins are leaf opening and closing, chloroplast movement, and the opening of stomata. However, of all responses controlled by phototropins, phototropism has been studied the longest and is the best understood.

In their 1880 treatise The Power of Movements in Plants, Charles Darwin and his son Francis first described phototropism as the bending of seedlings toward light. Darwin observed that light was perceived by the tip of the plant (the apical meristem), but that the response (bending) took place in a different part of the plant. They concluded that the signal had to travel from the apical meristem to the base of the plant.

In 1913, Peter Boysen-Jensen demonstrated that a chemical signal produced in the plant tip was responsible for the bending at the base. He cut off the tip of a seedling, covered the cut section with a layer of gelatin, and then replaced the tip. The seedling bent toward the light when illuminated. However, when impermeable mica flakes were inserted between the tip and the cut base, the seedling did not bend. A refinement of the experiment showed that the signal traveled on the shaded side of the seedling. When the mica plate was inserted on the illuminated side, the plant did bend towards the light. Therefore, the chemical signal was a growth stimulant because the phototropic response involved faster cell elongation on the shaded side than on the illuminated side. We now know that as light passes through a plant stem, it is diffracted and generates phototropin activation across the stem. Most activation occurs on the lit side, causing the plant hormone indole acetic acid (IAA) to accumulate on the shaded side. Stem cells elongate under influence of IAA.

Cryptochromes are another class of blue-light absorbing photoreceptors that also contain a flavin-based chromophore. Cryptochromes set the plants 24-hour activity cycle, also know as its circadian rhythem, using blue light cues. There is some evidence that cryptochromes work together with phototropins to mediate the phototropic response.

Use the navigation menu in the left panel of this website to view images of plants in motion.


Responses of photosynthetic capacity to soil moisture gradient in perennial rhizome grass and perennial bunchgrass

Changing water condition represents a dramatic impact on global terrestrial ecosystem productivity, mainly by limiting plant functions, including growth and photosynthesis, particularly in arid and semiarid areas. However, responses of the potential photosynthetic capacity to soil water status in a wide range of soil moisture levels, and determination of their thresholds are poorly understood. This study examined the response patterns of plant photosynthetic capacity and their thresholds to a soil moisture gradient in a perennial rhizome grass, Leymus chinensis, and a perennial bunchgrass, Stipa grandis, both dominant in the Eurasian Steppe.

Results

Severe water deficit produced negative effects on light-saturated net CO2 assimilation rate (Asat), stomatal conductance (gs), mesophyll conductance (gm), maximum carboxylation velocity (Vc,max), and maximal efficiency of PSII photochemistry (Fv/Fm). Photosynthetic activity was enhanced under moderate soil moisture with reductions under both severe water deficit and excessive water conditions, which may represent the response patterns of plant growth and photosynthetic capacity to the soil water gradient. Our results also showed that S. grandis had lower productivity and photosynthetic potentials under moderate water status, although it demonstrated generally similar relationship patterns between photosynthetic potentials and water status relative to L. chinensis.

Conclusions

The experiments tested and confirmed the hypothesis that responsive threshold points appear when plants are exposed to a broad water status range, with different responses between the two key species. It is suggested that vegetation structure and function may be shifted when a turning point of soil moisture occurs, which translates to terms of future climatic change prediction in semiarid grasslands.


Chapter 11 - Cell Communication

  • What messages are passed from cell to cell? How do cells respond to these messages?
  • We will first consider communication in microbes, to gain insight into the evolution of cell signaling.

Cell signaling evolved early in the history of life.

  • One topic of cell “conversation” is sex.
  • Saccharomyces cerevisiae, the yeast of bread, wine, and beer, identifies potential mates by chemical signaling.
    • There are two sexes, a and ?, each of which secretes a specific signaling molecule, a factor and ? factor, respectively.
    • These factors each bind to receptor proteins on the other mating type.
    • The molecular details of these pathways are strikingly similar in yeast and animal cells, even though their last common ancestor lived more than a billion years ago.
    • Signaling systems of bacteria and plants also share similarities.

    Communicating cells may be close together or far apart.

    • Multicellular organisms release signaling molecules that target other cells.
    • Cells may communicate by direct contact.
      • Both animals and plants have cell junctions that connect to the cytoplasm of adjacent cells.
      • Signaling substances dissolved in the cytosol can pass freely between adjacent cells.
      • Animal cells can communicate by direct contact between membrane-bound cell surface molecules.
      • Such cell-cell recognition is important to such processes as embryonic development and the immune response.
      • Some transmitting cells release local regulators that influence cells in the local vicinity.
      • One class of local regulators in animals, growth factors, includes compounds that stimulate nearby target cells to grow and multiply.
      • This is an example of paracrine signaling, which occurs when numerous cells simultaneously receive and respond to growth factors produced by a single cell in their vicinity.
      • The neurotransmitter stimulates the target cell.
      • The transmission of a signal through the nervous system can also be considered an example of long-distance signaling.
      • In animals, specialized endocrine cells release hormones into the circulatory system, by which they travel to target cells in other parts of the body.
      • Plant hormones, called growth regulators, may travel in vessels but more often travel from cell to cell or move through air by diffusion.
      • The plant hormone ethylene (C2H4), which promotes fruit ripening and regulates growth, is a hydrocarbon of only six atoms, capable of passing through cell walls.
      • Insulin, which regulates blood sugar levels in mammals, is a protein with thousands of atoms.
      • The signal must be recognized by a specific receptor molecule, and the information it carries must be changed into another form, or transduced, inside the cell before the cell can respond.

      The three stages of cell signaling are reception, transduction, and response.

      • E. W. Sutherland and his colleagues pioneered our understanding of cell signaling.
        • Their work investigated how the animal hormone epinephrine stimulates breakdown of the storage polysaccharide glycogen in liver and skeletal muscle.
        • Breakdown of glycogen releases glucose derivatives that can be used for fuel in glycolysis or released as glucose in the blood for fuel elsewhere.
        • Thus one effect of epinephrine, which is released from the adrenal gland during times of physical or mental stress, is mobilization of fuel reserves.
        • However, epinephrine did not activate the phosphorylase directly in vitro but could only act via intact cells.
        • Therefore, there must be an intermediate step or steps occurring inside the cell.
        • The plasma membrane must be involved in transmitting the epinephrine signal.
        • In reception, a chemical signal binds to a cellular protein, typically at the cell’s surface or inside the cell.
        • In transduction, binding leads to a change in the receptor that triggers a series of changes in a series of different molecules along a signal-transduction pathway. The molecules in the pathway are called relay molecules.
        • In response, the transduced signal triggers a specific cellular activity.

        Concept 11.2 Reception: A signal molecule binds to a receptor protein, causing it to change shape

        • The cell targeted by a particular chemical signal has a receptor protein on or in the target cell that recognizes the signal molecule.
          • Recognition occurs when the signal binds to a specific site on the receptor that is complementary in shape to the signal.
          • For other receptors, this causes aggregation of receptor molecules, leading to further molecular events inside the cell.

          Some receptor proteins are intracellular.

          • Some signal receptors are dissolved in the cytosol or nucleus of target cells.
            • To reach these receptors, the signals pass through the target cell’s plasma membrane.
            • Such chemical messengers are either hydrophobic enough or small enough to cross the phospholipid interior of the plasma membrane.
            • The cytosol of target cells contains receptor molecules that bind testosterone, activating the receptor.
            • These activated proteins enter the nucleus and turn on specific genes that control male sex characteristics.

            Most signal receptors are plasma membrane proteins.

            • Most signal molecules are water-soluble and too large to pass through the plasma membrane.
            • They influence cell activities by binding to receptor proteins on the plasma membrane.
              • Binding leads to changes in the shape of the receptor or to the aggregation of receptors.
              • These cause changes in the intracellular environment.
              • Seven alpha helices span the membrane.
              • G-protein-linked receptors bind many different signal molecules, including yeast mating factors, epinephrine and many other hormones, and neurotransmitters.
              • If GDP is bound to the G protein, the G protein is inactive.
              • When the appropriate signal molecule binds to the extracellular side of the receptor, the G protein binds GTP (instead of GDP) and becomes active.
              • The activated G protein dissociates from the receptor and diffuses along the membrane, where it binds to an enzyme, altering its activity.
              • The activated enzyme triggers the next step in a pathway leading to a cellular response.
              • This change turns the G protein off.
              • They play important roles during embryonic development.
              • Vision and smell in humans depend on these proteins.
              • Bacterial infections causing cholera and botulism interfere with G-protein function.
              • This system helps the cell regulate and coordinate many aspects of cell growth and reproduction.
              • A kinase is an enzyme that catalyzes the transfer of phosphate groups.
              • The cytoplasmic side of these receptors functions as a tyrosine kinase, transferring a phosphate group from ATP to tyrosine on a substrate protein.
              • An extracellular signal-binding site.
              • A single alpha helix spanning the membrane.
              • An intracellular tail with several tyrosines.
              • Ligands bind to two receptors, causing the two receptors to aggregate and form a dimer.
              • One tyrosine-kinase receptor dimer may activate ten or more different intracellular proteins simultaneously.
              • These activated relay proteins trigger many different transduction pathways and responses.
              • Binding by a ligand to the extracellular side changes the protein’s shape and opens the channel.
              • When the ligand dissociates from the receptor protein, the channel closes.
              • For example, neurotransmitter molecules released at a synapse between two neurons bind as ligands to ion channels on the receiving cell, causing the channels to open.
              • Ions flow in and trigger an electrical signal that propagates down the length of the receiving cell.

              Concept 11.3 Transduction: Cascades of molecular interactions relay signals from receptors to target molecules in the cell

              • The transduction stage of signaling is usually a multistep pathway.
              • These pathways often greatly amplify the signal.
                • If some molecules in a pathway transmit a signal to multiple molecules of the next component in the series, the result can be large numbers of activated molecules at the end of the pathway.

                Pathways relay signals from receptors to cellular responses.

                • Signal-transduction pathways act like falling dominoes.
                  • The signal-activated receptor activates another protein, which activates another, and so on, until the protein that produces the final cellular response is activated.
                  • The interaction of proteins is a major theme of cell signaling.
                  • Protein interaction is a unifying theme of all cellular regulation.
                  • It passes on information.
                  • At each step, the signal is transduced into a different form, often by a conformational change in a protein.
                  • The conformational change is often brought about by phosphorylation.

                  Protein phosphorylation, a common mode of regulation in cells, is a major mechanism of signal transduction.

                  • The phosphorylation of proteins by a specific enzyme (a protein kinase) is a widespread cellular mechanism for regulating protein activity.
                    • Most protein kinases act on other substrate proteins, unlike tyrosine kinases that act on themselves.
                    • Rarely, phosphorylation inactivates protein activity.
                    • Fully 2% of our genes are thought to code for protein kinases.
                    • Together, they regulate a large proportion of the thousands of cell proteins.
                    • These enzymes rapidly remove phosphate groups from proteins, a process called dephosphorylation.
                    • Phosphatases also make the protein kinases available for reuse, enabling the cell to respond again to a signal.

                    Certain signal molecules and ions are key components of signaling pathways (second messengers).

                    • Many signaling pathways involve small, water-soluble, nonprotein molecules or ions called second messengers.
                      • These molecules rapidly diffuse throughout the cell.
                      • Two of the most widely used second messengers are cyclic AMP and Ca2+.
                      • This occurs because the activated receptor activates adenylyl cyclase, which converts ATP to cAMP.
                      • The normal cellular concentration of cAMP can be boosted twentyfold within seconds.
                      • cAMP is short-lived, as phosphodiesterase converts it to AMP.
                      • Another surge of epinephrine is needed to reboost the cytosolic concentration of cAMP.
                      • Caffeine blocks the conversion of cAMP to AMP, maintaining the system in a state of activation in the absence of epinephrine.
                      • G-protein-linked receptors, G proteins, and protein kinases are other components of cAMP pathways.
                      • cAMP diffuses through the cell and activates a serine/threonine kinase called protein kinase A.
                      • The activated kinase phosphorylates various other proteins.
                      • These use a different signal molecule to activate a different receptor that activates an inhibitory G protein.
                      • The cholera bacterium, Vibrio cholerae, may be present in water contaminated with human feces.
                      • This bacterium colonizes the small intestine and produces a toxin that modifies a G protein that regulates salt and water secretion.
                      • The modified G protein is unable to hydrolyze GTP to GDP and remains stuck in its active form, continuously stimulating adenylyl cyclase to make cAMP.
                      • The resulting high concentration of cAMP causes the intestinal cells to secrete large amounts of water and salts into the intestines, leading to profuse diarrhea and death from loss of water and salts.
                      • One pathway uses cyclic GMP, or cGMP, as a signaling molecule. Its effects include the relaxation of smooth muscle cells in artery walls.
                      • A compound was developed to treat chest pains. This compound inhibits the hydrolysis of cGMP to GMP, prolonging the signal and increasing blood flow to the heart muscle.
                      • Under the trade name Viagra, this compound is now widely used as a treatment for erectile dysfunction. Viagra causes dilation of blood vessels, allowing increased blood flow to the penis.
                      • In animal cells, increases in Ca2+ may cause contraction of muscle cells, secretion of certain substances, and cell division.
                      • In plant cells, increases in Ca2+ trigger responses such as the pathway for greening in response to light.
                      • Various protein pumps transport Ca2+ outside the cell or into the endoplasmic reticulum or other organelles.
                      • As a result, the concentration of Ca2+ in the ER is usually much higher than the concentration in the cytosol.
                      • DAG and IP3 are created when a phospholipase cleaves membrane phospholipid PIP2.
                      • The phospholipase may be activated by a G protein or by a tyrosine-kinase receptor.
                      • IP3 activates a gated-calcium channel, releasing Ca2+ from the ER.

                      Concept 11.4 Response: Cell signaling leads to regulation of cytoplasmic activities or transcription

                      • Ultimately, a signal-transduction pathway leads to the regulation of one or more cellular activities.
                        • This may be the opening or closing of an ion channel or a change in cell metabolism.
                        • For example, epinephrine helps regulate cellular energy metabolism by activating enzymes that catalyze the breakdown of glycogen.

                        Elaborate pathways amplify and specify the cell’s response to signals.

                        • Signaling pathways with multiple steps have two benefits.
                          1. They amplify the response to a signal.
                          2. They contribute to the specificity of the response.
                        • At each catalytic step in a cascade, the number of activated products is much greater than in the preceding step.
                          • In the epinephrine-triggered pathway, binding by a small number of epinephrine molecules can lead to the release of hundreds of millions of glucose molecules.
                          • For example, epinephrine triggers liver or striated muscle cells to break down glycogen, but stimulates cardiac muscle cells to contract, leading to a rapid heartbeat.
                          • The response of a particular cell to a signal depends on its particular collection of receptor proteins, relay proteins, and proteins needed to carry out the response.
                          • Two cells that respond differently to the same signal differ in one or more of the proteins that handle and respond to the signal.
                          • Scaffolding proteins may themselves be relay proteins to which several other relay proteins attach.
                          • This hardwiring enhances the speed, accuracy, and efficiency of signal transfer between cells.
                          • The inherited disorder Wiskott-Aldrich syndrome (WAS) is caused by the absence of a single relay protein.
                          • Symptoms include abnormal bleeding, eczema, and a predisposition to infections and leukemia, due largely to the absence of the protein in the cells of the immune system.
                          • The WAS protein is located just beneath the cell surface, where it interacts with the microfilaments of the cytoskeleton and with several signaling pathways, including those that regulate immune cell proliferation.
                          • When the WAS protein is absent, the cytoskeleton is not properly organized and signaling pathways are disrupted.
                          • For a cell to remain alert and capable of responding to incoming signals, each molecular change in its signaling pathways must last only a short time.
                          • If signaling pathway components become locked into one state, whether active or inactive, the proper function of the cell can be disrupted.
                          • Binding of signal molecules to receptors must be reversible, allowing the receptors to return to their inactive state when the signal is released.
                          • Similarly, activated signals (cAMP and phosphorylated proteins) must be inactivated by appropriate enzymes to prepare the cell for a fresh signal.

                          Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 11-1


                          Plant Phototropism Experiment

                          As plants grow, they move up toward the light. But what is a plant&rsquos favorite color? Do plants move toward some colors more than others?

                          Problem

                          Do plants bend toward certain colors of light?

                          Materials

                          • 2 1-foot tall cardboard boxes with lids
                          • Piece of cardboard
                          • Ruler
                          • 2 small lamps
                          • 2 full spectrum light bulbs
                          • Box cutter knife
                          • Masking tape
                          • 1 3&rdquo x 3&rdquo piece of clear, red, green, and blue cellophane
                          • Water
                          • Spray bottle
                          • Camera
                          • 8 bean seeds
                          • 8 small pots

                          Procedure

                          1. First, get your plants growing. Plant two of your bean seeds in two different pots, water them, and wait for them to poke out of the ground.
                          2. While you&rsquore waiting, get your boxes ready. Cut a hole 2&rdquo in diameter about 3 inches from the bottom of each box. Place the clear cellophane over the hole. This will let all of the light into the box. Over the hole in the other box, place the red cellophane. This will only let red light into the box.
                          3. Put one plant in the first box and one in the second. Use a ruler to position each bean plant two inches away from the cellophane window. Take a photo of the plants, looking downward from the top of the box.
                          4. Put the boxes on different sides of the same room.
                          5. Now it&rsquos time to light things up! Put the lamps next to the boxes on the side with the cellophane window. Take out your ruler again and measure to make sure that the lamps are the same distance from the hole.
                          6. Put the lids on each box.
                          7. Every morning, turn on each lamp. Every night, turn off the lamps before you go to bed. Leave the plants to grow for a week.
                          8. After a week has passed, remove the lid and take a photo looking downward. Then remove the plants and take a photo from the front. Do the plants look different? Is one taller than the other? Is one twisted in a different direction?
                          9. Do the same experiment with new bean plants, but change the color of cellophane to blue. Finally, repeat the experiment with green cellophane.
                          10. Compare the photos of each bean plant after it had been growing for a week. Did the plants turn more toward a certain color? Was there a color they didn&rsquot like?

                          Results

                          The control plants will do better than the plants that are only exposed to one wavelength of light. The plants will grow better in red and blue light than in green light. The plants will grow toward red and blue light but will not move toward the green light.

                          Plants love the light, right? Yes and no. Plants do love the light, but they like some wavelengths of light more than others.

                          When you look at a rainbow, you can see that the visible spectrum of light actually has different colors or wavelengths inside it. The visible spectrum is the light that we can see. Different objects reflect different types of light. A blue bowl reflects blue light. A green plant reflects green light.

                          Inside a plant are chloroplasts. Inside the chloroplasts are tiny molecules called photopigments. Photopigments help the plant absorb light. A plant has different types of photopigments so it can absorb different colors of light.

                          When natural light shines on a plant, that plant takes in the light from the different wavelengths and uses it to make food. This natural light is called white light, and it contains all of the types of light. If there&rsquos only one color of light shining on a plant, then only some of the photopigments work, and the plant doesn&rsquot grow as well. This is why your plant under the full light spectrum grew better than the plants with the cellophane filters.

                          Plants also move toward the light. Seeds push little leaves up from the ground into the light. A house plant in a dark room will grow toward the light. This movement in response to light is called phototropism. When a plant moves toward the light, it&rsquos called positive tropism. When a plant moves away from light, it&rsquos called negative tropism.

                          How do plants move? They do so with the help of chemicals called auxins. Think of auxins as an elastic band for cells. They help cells get longer and move. Sunlight reduces auxin, so the areas of the plant that are exposed to sunlight will have less auxin. The areas on the dark side of the plant will have more auxin. That means that they will have long, stretchy cells. This allows the plant to move toward the light.

                          The plants in your experiment likely showed positive tropism, except when it came to the green light. Why did the plants not move toward the green light? Plants are green, which means that they reflect green light. It bounces off the leaves. This means that they can&rsquot use green light very well, and the green light bounces off the plant instead of encouraging movement toward the light.

                          Digging Deeper

                          What would happen if you left plants for a long time in light that was only red or blue? Would they survive?

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                          Disengagement of light responses in Arabidopsis by localized developmental factors

                          Plant development and growth are profoundly influenced by environmental cues such as light intensity and composition. In particular, changes in red (600 nm to 700 nm) and far-red (700 nm to 750 nm) light inform about the threat of competing plants nearby, which deplete red light and generate an unfavorable shade environment enriched in far-red light ( 1 ). Plants detect red and far-red light using an evolutionarily conserved family of photoreceptors named phytochromes, which are activated by red light and inactivated by far-red light ( 2 ). Phytochromes play an important role in shaping plant architecture, in part, by restricting the rate of stem growth ( 3 ). When plants encounter a canopy of neighboring plants, the far-red light-enriched shade environment inactivates phytochromes to promote stem growth, thereby allowing the plants to escape shade via the so-called shade avoidance response ( 4 , 5 ).

                          In the plant model species Arabidopsis thaliana (Arabidopsis), phytochromes are ubiquitously expressed in all tissue/organ types throughout the life cycle ( 6 ). This expression pattern enables all tissues/organs to continuously monitor and respond to changes in the local light environment. However, intriguingly, shade does not elicit growth in all stem tissues: While the embryonic stem (hypocotyl) and the leaf petiole are exquisitely sensitive to shade, the internodes—which are located at the boundary region connecting the hypocotyl, the bases of the leaves, and the shoot apical meristem—are almost completely unresponsive (Fig. 1A) ( 7 ). The lack of …


                          Hydrotropism

                          Hydrotropism is directional growth in response to water concentrations. This tropism is important in plants for protection against drought conditions through positive hydrotropism and against water over-saturation through negative hydrotropism. It is especially important for plants in arid biomes to be able to respond to water concentrations. Moisture gradients are sensed in plant roots. The cells on the side of the root closest to the water source experience slower growth than those on the opposite side. The plant hormone abscisic acid (ABA) plays an important role in inducing differential growth in the root elongation zone. This differential growth causes roots to grow toward the direction of water.

                          Before plant roots can exhibit hydrotropism, they must overcome their gravitrophic tendencies. This means that the roots must become less sensitive to gravity. Studies conducted on the interaction between gravitropism and hydrotropism in plants indicate that exposure to a water gradient or lack of water can induce roots to exhibit hydrotropism over gravitropism. Under these conditions, amyloplasts in root statocytes decrease in number. Fewer amyloplasts means that the roots are not as influenced by amyloplast sedimentation. Amyloplast reduction in root caps helps to enable roots to overcome the pull of gravity and move in response to moisture. Roots in well-hydrated soil have more amyloplasts in their root caps and have a much greater response to gravity than to water.


                          The Characteristics, Equation and Stages of Photosynthesis

                          The sun, the center of our planetary system and a star in the Milky Way galaxy (our galaxy), is the source of the energy processed and consumed by living organisms. Intense nuclear reactions in the sun release light and other energy radiation into the surrounding space. Some of this energy reaches our planet.

                          More Bite-Sized Q&As Below

                          2. How is light from the sun transformed into the chemical energy used by living organisms on earth?

                          Light from the sun is transformed into chemical energy contained in organic material through the process of photosynthesis. In photosynthesis, light, water and carbon dioxide react and highly energetic glucose molecules and molecular oxygen are produced. 

                          3. What is the chemical equation for photosynthesis?

                          The chemical equation for photosynthesis is the following:

                          Chloroplasts and Chlorophyll

                          4. What living organisms are responsible for photosynthesis?  What cell organelle is responsible for the absorption of light in the photosynthesis process in plants and algae?

                          There are many organisms (including all animals) that do not use photosynthesis. There are also autotrophic organisms that do not perform photosynthesis but which do perform chemosynthesis. Plants, algae and cyanobacteria are photosynthetic organisms.

                          In plants and algae, light is absorbed by chlorophyll, a molecule present in cytoplasmic organelles called chloroplasts.

                          5. Are there chloroplasts in cyanobacteria?

                          In cyanobacteria, there are no chloroplasts and chlorophyll layers are dispersed in the cytosol.

                          6. Which chemical element is at the center of the chlorophyll molecule?

                          The chemical element at the center of the chlorophyll molecule is magnesium. One atom of magnesium is present at the center of a combination of eight nitrogen-containing carbon rings. 

                          7. How do chloroplasts multiply?

                          Like mitochondria, chloroplasts have their own DNA, RNA and ribosomes and self-replicate through binary division.

                          8. What evidence is there to support the hypothesis that chloroplasts and mitochondria were primitive prokaryotes that developed a relationship of mutualism with primitive anaerobic eukaryotic cells? 

                          This hypothesis is known as the endosymbiotic hypothesis, and discusses the evolutionary origin of mitochondria and chloroplasts.

                          Mutualism is explained as the following in this context: mitochondria and chloroplasts can offer energy and nutrients to the cell in exchange for protection. This hypothesis is based  on the fact that those organelles have their own DNA, RNA and protein synthesis machinery and divide themselves through binary division like bacteria.

                          9. What are the main structures of chloroplasts?

                          Chloroplasts are made up of two membrane layers, the outer and the inner membranes. Inside the organelle, the basic unit is called the granum, and is a coin-shaped structure that, when combined with other grana, forms structures called thylakoids. Thylakoids fill the chloroplast and an intergrana membrane permeates the interior of the organelle.

                          10. In which chloroplast structure are chlorophyll molecules found?

                          Chlorophyll molecules are distributed in an organized manner in order to enhance the exposure of thylakoid surfaces to light.

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                          The Stages of Photosynthesis

                          11. What do ATP and ADP mean? What are the roles of these molecules in the energy metabolism of a cell?

                          ATP is the abbreviation of adenosine triphosphate, a molecule made of one adenosine molecule bound to three inorganic phosphate ions. ADP is an abbreviation of adenosine diphosphate, which is two molecules of phosphate bound to one molecule of adenosine. ATP stores energy for the cell. When ATP hydrolyzes and becomes ADP, energy is released and then consumed by several metabolic reactions.

                          12. What is ADP phosphorylation? What are photophosphorylation and oxidative phosphorylation?

                          ADP phosphorylation is the addition of one inorganic phosphate molecule to the adenosine diphosphate molecule, thus creating ATP (adenosine triphosphate) and incorporating energy. The phosphorylation is oxidative when the energy incorporated comes from the breaking down of organic molecules with oxygen as reagent, like in aerobic cellular respiration. The reaction is called photophosphorylation when the energy source is light, like in photosynthesis.

                          The energy incorporated into ATP is disposable (released) to other cellular reactions when ATP hydrolyzes and ADP is formed again. 

                          13. What are the stages of photosynthesis?

                          Photosynthesis is divided into the photochemical stage, or light reactions, and the chemical stage.

                          The Photochemical Stage of Photosynthesis

                          14. What are the processes that occur during the photochemical stage of photosynthesis?

                          The photolysis of water, the release of molecular oxygen, and the photophosphorylation of ADP, and the resulting of ATP and NADPH are the processes that occur during the photochemical stage of photosynthesis.

                          15. How is the light energy absorbed by chlorophyll transferred to ATP molecules during photophosphorylation? How is the resulting ATP used?

                          Light excites chlorophyll and energizes electrons that jump off the molecule. The energy released when these electrons escape is used in the phosphorylation of ADP, forming ATP. The enzyme that catalyzes the reaction is ATP synthase.

                          The resulting ATP is then consumed during the next chemical stage of photosynthesis to transfer energy to carbon dioxide for the formation of glucose. 

                          16. Is it correct to consider the breaking down of water through the action of light the basis of photosynthesis?

                          Besides ADP photophosphorylation, light energy is also responsible for the breaking down of water molecules during photosynthesis through a process known as water photolysis. During this reaction, water molecules are exposed to light energy and release protons (hydrogen ions), highly energetic electrons and molecular oxygen (O₂). Later, the hydrogen atoms bind to carbon dioxide molecules to form glucose. Since water is the hydrogen donor for photosynthesis, it is correct to say that water photolysis is the basis of the process.

                          17. What chemical substances are produced by water photolysis? What is the purpose of each of those substances?

                          Free electrons, hydrogen ions and molecular oxygen are released during water photolysis.

                          The electrons replace those electrons lost by chlorophyll molecules during photophosphorylation. The hydrogen ions are incorporated into hydrogen acceptor molecules (NADP) and later will be used in the synthesis of glucose during the chemical stage. Molecular oxygen is released into the atmosphere.

                          18. In sulfur photosynthetic bacteria, what molecule donates hydrogen for photosynthesis?

                          In sulfur photosynthetic bacteria, the substance that donates hydrogen is hydrogen sulfide (H₂S) and not water. Therefore, there is no release of molecular oxygen and instead molecular sulfur (S₂) is produced. (Oxygen and sulfur have the same number of valence electrons.)

                          19. Why people say that that during photosynthesis carbon dioxide is enriched by hydrogen atoms from water to form glucose?

                          During photosynthesis, carbon dioxide is energetically enriched by hydrogen obtained from water. Water broken down by photolysis is the hydrogen donor of the reaction. Glucose is made of carbon and oxygen atoms obtained from carbon dioxide as well as hydrogen atoms obtained from water. 

                          20. What is the complete chemical equation for photosynthesis?

                          The complete chemical equation of photosynthesis is the following:

                          6 CO₂ + 12 H₂O + light --> C₆H₁₂O₆ + 6 H₂O + 6 O₂

                          21. What is an example of a lab experiment that shows the variation in the efficiency of photosynthesis as a function of the different frequencies of light energy to which the reaction is exposed? Do you think that the green light frequency will be favorable to the reaction?

                          The experiment: Plants of same species and ages are each placed under (respecting their photoperiods) light sources emitting only one of the colors of the light spectrum (violet, indigo, blue, green, yellow and red). The experiment is carried out with each of the colors and, after days, each plant's development is compared. The plants whose development was normal performed satisfactory photosynthesis while those with abnormal development underused the light.

                          Chlorophyll is green because it reflects the green light frequency, meaning that it does not “use” the green range of the electromagnetic spectrum. Therefore, green light does not favor photosynthesis (strangely, green is the range of the light spectrum that plants “dislike”).

                          22. What are the divisions of white light according to the electromagnetic spectrum? Which are the two most efficient colors for photosynthesis?

                          The color divisions of the electromagnetic spectrum in decreasing order of frequency are: red, orange, yellow, green, blue, indigo and violet. When mixed together, these colors generate white.

                          It has been confirmed via experiments that the most useful colors for photosynthesis are blue and red.

                          23. What are NADP and NADPH?

                          NADP is the abbreviation for nicotinamide adenine dinucleotide phosphate cation, a hydrogen acceptor. NADPH is produced when NADP binds to one hydrogen atom. It is the form that transports hydrogen. 

                          24. Photosynthesis is the most important producer of molecular oxygen (O₂) on our planet. Which molecule do oxygen atoms released by photosynthesis come from? Which other molecule could you suspect they come from? Where do these oxygen atoms end up?

                          The oxygen atoms released as molecular oxygen through photosynthesis come from water.

                          It is easy to imagine that those oxygen atoms come from carbon dioxide. However, oxygen atoms from carbon dioxide are incorporated into glucose molecules and the water molecules released in the chemical stage of photosynthesis.

                          The Chemical Stage of Photosynthesis

                          25. Where do the photochemical and the chemical stages of photosynthesis occur?

                          The photochemical stage of photosynthesis occurs mainly in the thylakoids (the green part) and the chemical stage occurs in the stroma (the colorless framework) of the chloroplasts. 

                          26. Which byproducts of the photochemical stage are essential for the chemical stage of photosynthesis?

                          The chemical stage of photosynthesis depends on NADPH and ATP produced through “light reactions” (the photochemical stage). 

                          27. What are the roles of NADPH and ATP during the chemical stage of photosynthesis?

                          NADPH acts as a reductant of carbon dioxide, delivering highly energetic hydrogen atoms to precursor molecules during the glucose formation process. ATP is an energy source for the reactions of the chemical stage.

                          28. Why is the nickname “dark reactions” not entirely correct for the chemical stage of photosynthesis?

                          “Dark reactions” is not a correct name for the chemical stage of photosynthesis since the reactions of the chemical stage also occur in the presence of light.

                          29. What is the general chemical equation for photosynthesis? Why doesn't this equation clearly show the real origin of the molecular oxygen released?

                          The general equation for photosynthesis is:

                          6 CO₂ + 6 H₂O + light --> C₆H₁₂O₆ + 6 O₂

                          Water molecules are also produced during the chemical stage of photosynthesis as the following complete equation reveals:

                          6 CO₂ + 12 H₂O + light --> C₆H₁₂O₆ + 6 H₂O + 6 O₂

                          Water molecules are present on the reagent side as well on the product side of the equation. However, the pure mathematical simplification of stoichiometric coefficients leads to elimination of water from the product side, making it appear that 6 molecules of oxygen (O₂), that is, 12 atoms of oxygen, are made from the 6 molecules of water, that is, 6 oxygen atoms, in the reagent side. As a result, the false impression that 6 other oxygens atoms come from the carbon dioxide is created.

                          Limiting Factors of Photosynthesis

                          30. What are the three main limiting factors of photosynthesis?

                          The three main limiting factors of photosynthesis are light intensity, carbon dioxide concentration and temperature.

                          31. The rate at which photosynthesis takes place varies depending on the intensity of light energy. ਍oes the same occur in aerobic respiration? What is the effect of these variations on glucose balance?

                          In a photosynthetic organism, the rate of aerobic respiration can be superior, inferior or equal to the rate of photosynthesis. The rate of respiration depends on the energy needs of the plant while the rate of photosynthesis varies depending on the availability of light energy, if all other conditions are maintained the same.

                          In a situation in which the respiration rate is greater than the photosynthesis rate, glucose consumption is higher than glucose production. In a situation in which the respiration rate is lower than the photosynthesis rate, glucose is accumulated (positive balance). In a situation in which the rates are equal, all molecular oxygen produced by photosynthesis is used in respiration and all carbon dioxide released through respiration is consumed by photosynthesis. As a result, there is no positive balance of glucose or depletion of carbohydrate stores.

                          32. What is the compensation point? What is the importance of the compensation point for plant growth?

                          The (light) compensation point is the light energy intensity under which the aerobic respiration rate equals the photosynthesis rate. In this situation, all glucose produced is consumed and there is no incorporation of material into the plant. As a result, the plant stops growing. 

                          33. Why is carbon dioxide concentration a limiting factor in photosynthesis? When carbon dioxide concentration is increased indefinitely, is photosynthesis also increased indefinitely?

                          The availability of carbon dioxide is a limiting factor for photosynthesis because this gas is a reagent of the reaction.

                          Since enzymes catalyze the formation of organic molecules with carbon atoms from carbon dioxide, photosynthesis stops as soon as these enzymes become saturated, that is, when all their activation centers are bound to their substrates. In this situation, an increase in carbon dioxide concentration will not increase the photosynthesis rate.

                          34. Why do some trees lose their green color in the autumn?

                          In autumn, the days become shorter and nights become longer as a result, there is a reduction in the photosynthesis rate. Because of this, some plants prepare themselves for the winter by making nutrient stores. In this process, nutrients from the leaves travel to storage sites: branches, the trunk and roots. With less chlorophyll produced in leaves, the typical green color of the plant fades.

                          Now that you have finished studying Photosynthesis, these are your options:


                          11.4 Speciation

                          The biological definition of species, which works for sexually reproducing organisms, is a group of actually or potentially interbreeding individuals. According to this definition, one species is distinguished from another by the possibility of matings between individuals from each species to produce fertile offspring. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In fact, the presence of hybrids between similar species suggests that they may have descended from a single interbreeding species and that the speciation process may not yet be completed.

                          Given the extraordinary diversity of life on the planet there must be mechanisms for speciation : the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found in On the Origin of Species (Figure 11.14a). For speciation to occur, two new populations must be formed from one original population, and they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric speciation , meaning speciation in “other homelands,” involves a geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation , meaning speciation in the “same homeland,” involves speciation occurring within a parent species while remaining in one location.

                          Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why there might not be more than two species formed at one time except that it is less likely and such multiple events can also be conceptualized as single splits occurring close in time.

                          Speciation through Geographic Separation

                          A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous that free-flow of alleles is prevented. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors, for the two populations will differ causing natural selection to favor divergent adaptations in each group. Different histories of genetic drift, enhanced because the populations are smaller than the parent population, will also lead to divergence.

                          Given enough time, the genetic and phenotypic divergence between populations will likely affect characters that influence reproduction enough that were individuals of the two populations brought together, mating would be less likely, or if a mating occurred, offspring would be non-viable or infertile. Many types of diverging characters may affect the reproductive isolation (inability to interbreed) of the two populations. These mechanisms of reproductive isolation can be divided into prezygotic mechanisms (those that operate before fertilization) and postzygotic mechanisms (those that operate after fertilization). Prezygotic mechanisms include traits that allow the individuals to find each other, such as the timing of mating, sensitivity to pheromones, or choice of mating sites. If individuals are able to encounter each other, character divergence may prevent courtship rituals from leading to a mating either because female preferences have changed or male behaviors have changed. Physiological changes may interfere with successful fertilization if mating is able to occur. Postzygotic mechanisms include genetic incompatibilities that prevent proper development of the offspring, or if the offspring live, they may be unable to produce viable gametes themselves as in the example of the mule, the infertile offspring of a female horse and a male donkey.

                          If the two isolated populations are brought back together and the hybrid offspring that formed from matings between individuals of the two populations have lower survivorship or reduced fertility, then selection will favor individuals that are able to discriminate between potential mates of their own population and the other population. This selection will enhance the reproductive isolation.

                          Isolation of populations leading to allopatric speciation can occur in a variety of ways: from a river forming a new branch, erosion forming a new valley, or a group of organisms traveling to a new location without the ability to return, such as seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are that individuals from each population would fly back and forth, continuing gene flow. However, if two rodent populations became divided by the formation of a new lake, continued gene flow would be unlikely therefore, speciation would be more likely.

                          Biologists group allopatric processes into two categories. If a few members of a species move to a new geographical area, this is called dispersal . If a natural situation arises to physically divide organisms, this is called vicariance .

                          Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United States, two separate subspecies of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative, the Mexican spotted owl, which lives in the south (Figure 11.15). The cause of their initial separation is not clear, but it may have been caused by the glaciers of the ice age dividing an initial population into two. 5

                          Additionally, scientists have found that the further the distance between two groups that once were the same species, the more likely for speciation to take place. This seems logical because as the distance increases, the various environmental factors would likely have less in common than locations in close proximity. Consider the two owls in the north, the climate is cooler than in the south the other types of organisms in each ecosystem differ, as do their behaviors and habits also, the hunting habits and prey choices of the owls in the south vary from the northern ones. These variances can lead to evolved differences in the owls, and over time speciation will likely occur unless gene flow between the populations is restored.

                          In some cases, a population of one species disperses throughout an area, and each finds a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species, which is called adaptive radiation . From one point of origin, many adaptations evolve causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island, which leads to geographical isolation for many organisms (Figure 11.16). The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved, including the eight shown in Figure 11.16.

                          Notice the differences in the species’ beaks in Figure 11.16. Change in the genetic variation for beaks in response to natural selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source. The fruit and seed-eating birds have thicker, stronger beaks which are suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach their nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. Darwin’s finches are another well-studied example of adaptive radiation in an archipelago.

                          Concepts in Action

                          Click through this interactive site to see how island birds evolved click to see images of each species in evolutionary increments from five million years ago to today.

                          Speciation without Geographic Separation

                          Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same habitat? A number of mechanisms for sympatric speciation have been proposed and studied.

                          One form of sympatric speciation can begin with a chromosomal error during meiosis or the formation of a hybrid individual with too many chromosomes. Polyploidy is a condition in which a cell, or organism, has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploid state. In some cases a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy (Figure 11.17). The prefix “auto” means self, so the term means multiple chromosomes from one’s own species. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating.

                          For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes produced by this plant species. But they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4n called a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species. The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid. The prefix “allo” means “other” (recall from allopatric) therefore, an allopolyploid occurs when gametes from two different species combine. Figure 11.18 illustrates one possible way an allopolyploidy can form. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results.

                          The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, most chromosomal abnormalities in animals are lethal it takes place most commonly in plants. Scientists have discovered more than 1/2 of all plant species studied relate back to a species evolved through polyploidy.

                          Sympatric speciation may also take place in ways other than polyploidy. For example, imagine a species of fish that lived in a lake. As the population grew, competition for food also grew. Under pressure to find food, suppose that a group of these fish had the genetic flexibility to discover and feed off another resource that was unused by the other fish. What if this new food source was found at a different depth of the lake? Over time, those feeding on the second food source would interact more with each other than the other fish therefore they would breed together as well. Offspring of these fish would likely behave as their parents and feed and live in the same area, keeping them separate from the original population. If this group of fish continued to remain separate from the first population, eventually sympatric speciation might occur as more genetic differences accumulated between them.

                          This scenario does play out in nature, as do others that lead to reproductive isolation. One such place is Lake Victoria in Africa, famous for its sympatric speciation of cichlid fish. Researchers have found hundreds of sympatric speciation events in these fish, which have not only happened in great number, but also over a short period of time. Figure 11.19 shows this type of speciation among a cichlid fish population in Nicaragua. In this locale, two types of cichlids live in the same geographic location however, they have come to have different morphologies that allow them to eat various food sources.

                          Finally, a well-documented example of ongoing sympatric speciation occurred in the apple maggot fly, Rhagoletis pomonella, which arose as an isolated population sometime after the introduction of the apple into North America. The native population of flies fed on hawthorn species and is host-specific: it only infests hawthorn trees. Importantly, it also uses the trees as a location to meet for mating. It is hypothesized that either through mutation or a behavioral mistake, flies jumped hosts and met and mated in apple trees, subsequently laying their eggs in apple fruit. The offspring matured and kept their preference for the apple trees effectively dividing the original population into two new populations separated by host species, not by geography. The host jump took place in the nineteenth century, but there are now measureable differences between the two populations of fly. It seems likely that host specificity of parasites in general is a common cause of sympatric speciation.


                          Julin N. Maloof

                          Light is essential for plant growth. Perhaps as a consequence, plants have an intricate set of photoreceptors and responses that they use to optimize their development and physiology to suit their light environment. We study the downstream mechanisms underlying these responses and how plants have evolved differences in their light perception and responses that allow them to thrive in different environments. We are interested in both the genetic and molecular basis of variation in light response as well as the adaptive consequences. A combination of molecular and quantitative genetics and genomics is used in Arabidopsis, Tomato, and Brassica

                          Grad Group Affiliations

                          Specialties / Focus

                          • Cell and Developmental Biology
                          • Environmental and Integrative Biology
                          • Integrated Genetics and Genomics
                          • Model Plants
                          • Molecular Biology, Biochemistry and Genomics
                          • Plant Breeding
                          • Quantitative and Population Genetics

                          Courses

                          Honors and Awards

                          Professional Societies

                          • Genetics Society of America
                          • American Society of Plant Biologists
                          • American Association for the Advancement of Science

                          Degrees

                          • 1989 BA Biology Haverford College
                          • 1998 PhD Biochemistry University of California, San Francisco

                          Publications

                          Nohales MA, Liu W, Duffy T, Nozue K, Sawa M, Pruneda-Paz JL, Maloof JN, Jacobsen SE, Kay SA. Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock. Dev. Cell. 2019 Jun 1749(6):840-851.e8.

                          Baker RL, Leong WF, Brock MT, Rubin MJ, Markelz RJC, Welch S, Maloof JN, Weinig C. Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLOS Genetics. 2019 Sep 1215(9):e1008367.

                          Amini H, Naghavi MR, Shen T, Wang Y, Nasiri J, Khan IA, Fiehn O, Zerbe P, Maloof JN. Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida. G3: Genes, Genomes, Genetics. 2019 Mar 19(3):807–16.

                          Schrager‐Lavelle A, Gath NN, Devisetty UK, Carrera E, López‐Díaz I, Blázquez MA, Maloof JN. The role of a class III gibberellin 2-oxidase in tomato internode elongation. The Plant Journal [Internet]. 2018 [cited 2019 Jan 17]0(0). Retrieved from: https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14145

                          Nozue K, Devisetty UK, Lekkala S, Mueller-Moulé P, Bak A, Casteel CL, Maloof JN. Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance. Plant Physiology. 2018 Dec 1178(4):1720–32.

                          Li R, Jeong K, Davis JT, Kim S, Lee S, Michelmore RW, Kim S, Maloof JN. Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus. Front. Plant Sci. [Internet]. 2018 [cited 2019 Jan 17]9. Retrieved from: https://www.frontiersin.org/articles/10.3389/fpls.2018.01632/full

                          Wang Z, Yang R, Devisetty UK, Maloof JN, Zuo Y, Li J, Shen Y, Zhao J, Bao M, Ning G. The Divergence of Flowering Time Modulated by FT/TFL1 Is Independent to Their Interaction and Binding Activities. Front. Plant Sci. [Internet]. 2017 [cited 2017 Jun 19]8. Retrieved from: http://journal.frontiersin.org/article/10.3389/fpls.2017.00697/full

                          Rubin Matthew J., Brock Marcus T., Davis Amanda M., German Zachary M., Knapp Mary, Welch Stephen M., Harmer Stacey L., Maloof Julin N., Davis Seth J., Weinig Cynthia. Circadian rhythms vary over the growing season and correlate with fitness components. Molecular Ecology. 2017 Aug 926(20):5528–40.

                          Markelz RJC, Covington MF, Brock MT, Devisetty UK, Kliebenstein DJ, Weinig C, Maloof JN. Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3: Genes, Genomes, Genetics. 2017 Jul 17(7):2259–70.

                          Filiault D, Seymour D, Maruthachalam R, Maloof J. The Generation of Doubled Haploid Lines for QTL Mapping. In: Busch W, editor. Plant Genomics [Internet]. Springer New York 2017. p. 39–57. Retrieved from: http://dx.doi.org/10.1007/978-1-4939-7003-2_4

                          Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. Front. Plant Sci. [Internet]. 2017 [cited 2018 Jan 29]8. Retrieved from: https://www.frontiersin.org/articles/10.3389/fpls.2017.00900/full

                          Schrager-Lavelle A, Herrera LA, Maloof JN. Tomato phyE Is Required for Shade Avoidance in the Absence of phyB1 and phyB2. Frontiers in Plant Science. 20167:1275.

                          Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L, Ichihashi Y, Zumstein K, Maloof JN, Sinha NR. eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. Plant Physiol. 2016 Sep 1172(1):328–40.

                          Nguyen TT, Slaughter DC, Maloof JN, Sinha N. Plant phenotyping using multi-view stereo vision with structured lights. 2016 [cited 2016 May 27]. p. 986608-986608–9. Retrieved from: http://dx.doi.org/10.1117/12.2229513

                          Müller-Moulé P, Nozue K, Pytlak ML, Palmer CM, Covington MF, Wallace AD, Harmer SL, Maloof JN. YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance. PeerJ. 2016 Oct 134:e2574.

                          Müller NA, Wijnen CL, Srinivasan A, Ryngajllo M, Ofner I, Lin T, Ranjan A, West D, Maloof JN, Sinha NR, Huang S, Zamir D, Jiménez-Gómez JM. Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat. Genet. 2016 Jan48(1):89–93.

                          Kohnen MV, Schmid-Siegert E, Trevisan M, Petrolati LA, Sénéchal F, Müller-Moulé P, Maloof J, Xenarios I, Fankhauser C. Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth. Plant Cell. 2016 Dec 128(12):2889–904.

                          Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, Sinha NR. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3. 2016 Oct 16(10):3169–84.

                          Carriedo LG, Maloof JN, Brady SM. Molecular control of crop shade avoidance. Curr. Opin. Plant Biol. 2016 Mar 2330:151–8.

                          Brock MT, Lucas LK, Anderson NA, Rubin MJ, Cody Markelz RJ, Covington MF, Devisetty UK, Chapple C, Maloof JN, Weinig C. Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning. Mol. Ecol. 2016 Mar25(5):1122–40.

                          Rellán-Álvarez R, Lobet G, Lindner H, Pradier P-L, Sebastian J, Yee M-C, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, Dinneny JR. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife. 2015 Aug 194:e07597.

                          Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling. PLoS Genet. 2015 Apr 1511(4):e1004953.

                          Nguyen TT, Slaughter DC, Max N, Maloof JN, Sinha N. Structured Light-Based 3D Reconstruction System for Plants. Sensors. 2015 Jul 2915(8):18587–612.

                          Chitwood DH, Kumar R, Ranjan A, Pelletier JM, Townsley BT, Ichihashi Y, Martinez CC, Zumstein K, Harada JJ, Maloof JN, Sinha NR. Light-Induced Indeterminacy Alters Shade-Avoiding Tomato Leaf Morphology. Plant Physiol. 2015 Nov 1169(3):2030–47.

                          Bush SM, Carriedo L, Daniel F, Ichihashi Y, Covington MF, Kumar R, Ranjan A, Chitwood DH, Headland L, Filiault DL, Jimenez-Gomez JM, Sinha NR, Maloof JN. Auxin signaling is a common factor underlying natural variation in tomato shade avoidance. bioRxiv. 2015 Nov 23031088.

                          Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ. Reassess the t Test: Interact with All Your Data via ANOVA. Plant Cell. 2015 Jul 28tpc.15.00238.

                          Baker RL, Leong WF, Brock MT, Markelz RJC, Covington MF, Devisetty UK, Edwards CE, Maloof J, Welch S, Weinig C. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytologist. 2015 Oct208(1):257–68.

                          Ichihashi Y, Aguilar-Martínez JA, Farhi M, Chitwood DH, Kumar R, Millon LV, Peng J, Maloof JN, Sinha NR. Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proceedings of the National Academy of Sciences. 2014 Jun111(25):E2616–21.

                          Fitz Gerald JN, Carlson AL, Smith E, Maloof JN, Weigel D, Chory J, Borevitz JO, Swanson RJ. New Arabidopsis advanced intercross recombinant inbred lines reveal female control of nonrandom mating. PLANT PHYSIOLOGY. 2014 May165(1):175–185.

                          Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN. Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing. G3. 2014 Nov 14(11):2065–78.

                          Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland LR, Ostria-Gallardo E, Aguilar-Martínez JA, Bush S, Carriedo L, Fulop D, Martinez CC, Peng J, Maloof JN, Sinha NR. Resolving Distinct Genetic Regulators of Tomato Leaf Shape within a Heteroblastic and Ontogenetic Context. Plant Cell. 2014 Sep 126(9):3616–29.

                          Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya M, Prins B, Li L, Myles S, Sinha NR. A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. PLANT PHYSIOLOGY. 2014 Jan164(1):259–272.

                          Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Gómez JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics. 2014 Sep46(9):1034–1038.

                          Sharlach M, Dahlbeck D, Liu L, Chiu J, Jiménez-Gómez JM, Kimura S, Koenig D, Maloof JN, Sinha N, Minsavage GV, Jones JB, Stall RE, Staskawicz BJ. Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Theor Appl Genet. 2013 Mar 1126(3):601–9.

                          Ron M, Dorrity MW, Lucas M de, Toal T, Hernandez RI, Little SA, Maloof JN, Kliebenstein DJ, Brady SM. Identification of Novel Loci Regulating Interspecific Variation in Root Morphology and Cellular Development in Tomato. Plant Physiol. 2013 Jun 1162(2):755–68.

                          Maloof JN, Nozue K, Mumbach MR, Palmer CM. LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement. Journal of Visualized Experiments [Internet]. 2013(71). Retrieved from: http://www.jove.com/video/50028/leafj-an-imagej-plugin-for-semi-automated-leaf-shape-measurement

                          Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. PNAS. 2013 Jul 9110(28):E2655–62.

                          Chitwood DH, Maloof JN, Sinha NR. Dynamic Transcriptomic Profiles between Tomato and a Wild Relative Reflect Distinct Developmental Architectures. Plant Physiol. 2013 Jun 1162(2):537–52.

                          Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR. A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines. Plant Cell. 2013 Jul 125(7):2465–81.

                          Seymour DK, Filiault DL, Henry IM, Monson-Miller J, Ravi M, Pang A, Comai L, Chan SWL, Maloof JN. Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proceedings of the National Academy of Sciences of the United States of America. 2012 Mar109(11):4227–4232.

                          Palmer CM, Bush SM, Maloof JN. Phenotypic and Developmental Plasticity in Plants. eLS [Internet]. John Wiley & Sons. Ltd: Chichester 2012. p. 1–9. Retrieved from: http://onlinelibrary.wiley.com/store/10.1002/9780470015902.a0002092.pub2/asset/a0002092.pdf?v=1&t=h98v932v&s=207c34561dbf8ad8be1d4db3bec3e429e7148429

                          Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN, Sinha NR. A High-Throughput Method for Illumina RNA-Seq Library Preparation. Frontiers in plant science. 20123:202.

                          Filiault DL, Maloof JN. A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response. PLoS Genetics. 2012 Mar8(3):e1002589.

                          Chitwood DH, Headland LR, Kumar R, Peng J, Maloof JN, Sinha NR. The Developmental Trajectory of Leaflet Morphology in Wild Tomato Species. Plant Physiol. 2012 Mar 1158(3):1230–40.

                          Chitwood DH, Headland LR, Filiault DL, Kumar R, Jiménez-Gómez JM, Schrager AV, Park DS, Peng J, Sinha NR, Maloof JN. Native Environment Modulates Leaf Size and Response to Simulated Foliar Shade across Wild Tomato Species. PloS one. 20127(1):e29570.

                          Stewart JL, Maloof JN, Nemhauser JL. PIF genes mediate the effect of sucrose on seedling growth dynamics. PloS one. 20116(5):e19894.

                          Nozue K, Harmer SL, Maloof JN. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis. PLANT PHYSIOLOGY. 2011 May156(1):357–372.

                          Kim K, Shin J, Lee S-H, Kweon H-S, Maloof JN, Choi G. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proceedings of the National Academy of Sciences of the United States of America. 2011 Jan108(4):1729–1734.

                          Kerwin RE, Jiménez-Gómez JM, Fulop D, Harmer SL, Maloof JN, Kliebenstein DJ. Network quantitative trait loci mapping of circadian clock outputs identifies metabolic pathway-to-clock linkages in Arabidopsis. THE PLANT CELL. 2011 Feb23(2):471–485.

                          Jiménez-Gómez JM, Corwin JA, Joseph B, Maloof JN, Kliebenstein DJ. Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genetics. 2011 Sep7(9):e1002295.

                          Holtan HE, Bandong S, Marion CM, Adam L, Tiwari S, Shen Y, Maloof JN, Maszle DR, Ohto M-A, Preuss S, Meister R, Petracek M, Repetti PP, Reuber TL, Ratcliffe OJ, Khanna R. BBX32, an Arabidopsis B-Box protein, functions in light signaling by suppressing HY5-regulated gene expression and interacting with STH2/BBX21. PLANT PHYSIOLOGY. 2011 Aug156(4):2109–2123.

                          Chang C-SJ, Maloof JN, Wu S-H. COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. PLANT PHYSIOLOGY. 2011 May156(1):228–239.

                          Arana MV, Marín-de la Rosa N, Maloof JN, Blázquez MA, Alabadí D. Circadian oscillation of gibberellin signaling in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2011 May108(22):9292–9297.

                          Maloof JN. Recent advances in regulation of flowering. F1000 biology reports [Internet]. 20102. Retrieved from: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20948781&retmode=ref&cmd=prlinks

                          Jiménez-Gómez JM, Wallace AD, Maloof JN. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genetics. 2010 Sep6(9):e1001100.

                          Brock MT, Maloof JN, Weinig C. Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana. Molecular ecology. 2010 Mar19(6):1187–1199.

                          Brock MT, Dechaine JM, Iniguez-Luy FL, Maloof JN, Stinchcombe JR, Weinig C. Floral genetic architecture: an examination of QTL architecture underlying floral (co)variation across environments. Genetics. 2010 Dec186(4):1451–1465.

                          Schwartz C, Balasubramanian S, Warthmann N, Michael TP, Lempe J, Sureshkumar S, Kobayashi Y, Maloof JN, Borevitz JO, Chory J, Weigel D. Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana. Genetics. 2009 Oct183(2):723–32, 1SI–7SI.

                          Jiménez-Gómez JM, Maloof JN. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC plant biology. 20099:85.

                          Jiménez-Gómez JM, Maloof JN. Plant research accelerates along the (bio)informatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO reports [Internet]. Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616, USA. 2009. p. 568–572. Retrieved from: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19465891&retmode=ref&cmd=prlinks

                          Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, Weigel D. QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PloS one. 20094(2):e4318.

                          Filiault DL, Wessinger CA, Dinneny JR, Lutes J, Borevitz JO, Weigel D, Chory J, Maloof JN. Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proceedings of the National Academy of Sciences of the United States of America. 2008 Feb105(8):3157–3162.

                          Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome biology. 20089(8):R130.

                          Weinig C, Johnston JA, Willis CG, Maloof JN. Antagonistic multilevel selection on size and architecture in variable density settings. Evolution international journal of organic evolution. 2007 Jan61(1):58–67.

                          Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, Harmer SL, Maloof JN. Rhythmic growth explained by coincidence between internal and external cues. Nature. 2007 Jul448(7151):358–361.

                          Nozue K, Maloof JN. Diurnal regulation of plant growth. Plant, cell & environment. 2006 Mar29(3):396–408.

                          Maloof JN. Small but not forgotten. Heredity. 2006 Jan96(1):1–2.

                          Balasubramanian S, Sureshkumar S, Agrawal M, Michael TP, Wessinger C, Maloof JN, Clark R, Warthmann N, Chory J, Weigel D. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nature Genetics. 2006 Jun38(6):711–715.

                          Lu L, Lee Y-RJ, Pan R, Maloof JN, Liu B. An internal motor kinesin is associated with the Golgi apparatus and plays a role in trichome morphogenesis in Arabidopsis. Molecular biology of the cell. 2005 Feb16(2):811–823.

                          Maloof JN. Plant development: slowing root growth naturally. 2004 May14(10):R395–6.

                          Nemhauser JL, Maloof JN, Chory J. Building integrated models of plant growth and development. PLANT PHYSIOLOGY. 2003 Jun132(2):436–439.

                          Maloof JN. QTL for plant growth and morphology. Current opinion in plant biology. 2003 Feb6(1):85–90.

                          Maloof JN. Genomic approaches to analyzing natural variation in Arabidopsis thaliana. Current opinion in genetics & development. 2003 Dec13(6):576–582.

                          Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genetics. 2002 Feb30(2):190–193.

                          Friedrichsen DM, Nemhauser J, Muramitsu T, Maloof JN, Alonso J, Ecker JR, Furuya M, Chory J. Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics. 2002 Nov162(3):1445–1456.

                          Borevitz JO, Maloof JN, Lutes J, Dabi T, Redfern JL, Trainer GT, Werner JD, Asami T, Berry CC, Weigel D, Chory J. Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics. 2002 Feb160(2):683–696.

                          Maloof JN, Borevitz JO, Dabi T, Lutes J, Nehring RB, Redfern JL, Trainer GT, Wilson JM, Asami T, Berry CC, Weigel D, Chory J. Natural variation in light sensitivity of Arabidopsis. Nature Genetics. 2001 Dec29(4):441–446.

                          Maloof JN, Borevitz JO, Weigel D, Chory J. Natural variation in phytochrome signaling. Seminars in cell & developmental biology. 2000 Dec11(6):523–530.

                          Schlesinger A, Shelton CA, Maloof JN, Meneghini M, Bowerman B. Wnt pathway components orient a mitotic spindle in the early Caenorhabditis elegans embryo without requiring gene transcription in the responding cell. Genes & development. 1999 Aug13(15):2028–2038.

                          Maloof JN, Whangbo J, Harris JM, Jongeward GD, Kenyon C. A Wnt signaling pathway controls hox gene expression and neuroblast migration in C. elegans. Development (Cambridge, England). 1999 Jan126(1):37–49.

                          Hunter CP, Harris JM, Maloof JN, Kenyon C. Hox gene expression in a single Caenorhabditis elegans cell is regulated by a caudal homolog and intercellular signals that inhibit wnt signaling. Development (Cambridge, England). 1999 Feb126(4):805–814.

                          Maloof JN, Kenyon C. The Hox gene lin-39 is required during C. elegans vulval induction to select the outcome of Ras signaling. Development (Cambridge, England). 1998 Jan125(2):181–190.

                          Eisenmann DM, Maloof JN, Simske JS, Kenyon C, Kim SK. The beta-catenin homolog BAR-1 and LET-60 Ras coordinately regulate the Hox gene lin-39 during Caenorhabditis elegans vulval development. Development (Cambridge, England). 1998 Sep125(18):3667–3680.

                          Kenyon CJ, Austin J, Costa M, Cowing DW, Harris JM, Honigberg L, Hunter CP, Maloof JN, Muller-Immerglück MM, Salser SJ, Waring DA, Wang BB, Wrischnik LA. The dance of the Hox genes: patterning the anteroposterior body axis of Caenorhabditis elegans. Cold Spring Harbor symposia on quantitative biology. 199762:293–305.

                          Chavez RA, Maloof J, Beeson D, Newsom-Davis J, Hall ZW. Subunit folding and alpha delta heterodimer formation in the assembly of the nicotinic acetylcholine receptor. Comparison of the mouse and human alpha subunits. The Journal of biological chemistry. 1992 Nov267(32):23028–23034.


                          Plant Physiology and Biochemistry

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