QUESTION FROM WELLY SANJAYA (INDONESIA EAST JAVA):   I want to know about riceplant education.

DR. CAROLYN:   Hi, Welly. Gramene has a great educational outreach page on rice. See http://www.gramene.org/species/oryza/rice_intro.html. Information about the anatomy, taxonomy, news, germplasm resources, etc. are all available there. Good luck!


QUESTION FROM STEVE WAGNER (SEMINOLE, FLORIDA):   I'm teaching a high school research class to go along with my senior ap biology class. Some of my students are interested in working with tomatoes (probably because they know I love growing, experimenting with and eating tomatoes). I've suggested various topics, but would appreciate any you might suggest. Some I've already suggested include antimicrobial properties of leaf extracts, effects of: various salinities on growth, productivity, etc; different colored mulches, foliar nutrient sprays, vitamin applications, root pruning, pH, photoperiod, interplanting with legumes, cross breeding for enhanced sugar production, and others. To me, these seem to run-of -the-mill. Any help with additonal ideas would be greatly appreciated. Thanks for any suggestions you could make.

DR. CAROLYN:   What wonderful ideas you already have, Steve! I can't promise that my ideas are any better, but they'll increase the breadth of things you could encourage your students to try.

1. Chemical pest treatments across different tomato genotypes and potentially with some plants in screened cages to provide physical barriers to pests.
2. Effects of plant hormones (auxins and/or cytokinins) on growth of different tomato genotypes.
3. Yield from tomatoes grown organic versus ones grown with commercial fertilizers and pest control agents.
4. Yield from tomatoes grown on hydroponics versus ones grown in soil.

Good luck!!!


QUESTION FROM NATHAN (IN THE UK):   Are the ESTs for A. lyrata specific to that species, or could I expect to find orthologs in other Arabidopsis species? Also, which subspecies of lyrata are the ESTs [stored at PlantGDB] from?

DR. CAROLYN:   Let me answer your questions in reverse order. At PlantGDB the sequences are categorized by species: the subspecies information generally is not taken into account. The only way to decide whether a given sequence is from a particular subspecies is to view the original sequence records of interest directly. You will find that subspecies designations are rarely attached to the sequence records by the submitter.

Now for your first set of questions: the ESTs for A. lyrata all came from that species, but the sequences cannot be assumed to be unique to the species without further investigation. However, certainly you should expect to find sequences orthologous to A. lyrata sequences in other Arabidopsis species. To help you to understand why this is the case, let me define some evolutionary terms. Two sequences are homologous if they are related by descent (i.e., if they originate from the same ancestral sequence). Within the group called homologs are paralogs and orthologs. Paralogs are sequences that are related by a duplication within a given genome, and paralogs often evolve new function over evolutionary time. Orthologs are sequences in different species that evolved from a common ancestral sequence by speciation. The functions of two orthologous sequences are expected to be the same. Because all species within the Arabidopsis genus are related by descent, you should expect to find orthologous sequences quite easily among these species. For a diagram that depicts the meaning of these three terms, see this figure at NCBI.


QUESTION FROM KIRSTI (IN SOUTHERN CA):   Where is the phytochrome gene/family of genes located in the plant genome? How would one go about isolating (extracting) this gene for PCR in several plant species?

DR. CAROLYN:   Actually, whether a plant has one or many copies of members of the phytochrome gene family varies by species, and where the gene(s) exist within the genome is also highly variable, and in most plants is probably largely unknown. Different plants have arranged their genomes in different ways, a phenomenon evident on a large scale when you consider that different plants have different numbers of chromosomes. Even if all plants had only one copy of phytochrome in the genome it could be on chromosome 1 near a centromere in one species, and on chromosome 10 near a telomere in another.

For the second part of your question, I would not try to isolate a gene and then do PCR. Instead I would do PCR using degenerate primers to amplify genomic DNA, then clone the amplified fragment into a bacterial plasmid for safekeeping. To do degenrate PCR, you would look at the protein sequence of known representatives of the gene family and identify two amino acid subsequences (one at the amino end of the protein sequence and another toward the carboxy terminus) that are conserved among all known members of the gene family. Then design primers that would amplify any of the codons that might encode those amino acids. For a more detailed explanation of how degenerate PCR works, see this guide.


QUESTION FROM CHRIS S.:   In my genetics class we are learning about dihybrid crosses, and I still don't quite get it.

DR. CAROLYN:   I poked around online a bit and found a really good interactive website you can try out that might help! Go here, and walk through the demonstration. Maybe doing it a few times in tandem with reviewing your textbook and notes will help out a bit. (I should point out that in the demonstration, the pea sperm are drawn to look flagellated... The sperm of flowering plants are not flagellated, so the demo is flawed. Otherwise it's a realistic representation and should help you to figure out how dihybrid crosses work in general.)


QUESTION FROM LYN:   Is the sequence listed at GenBank the template for transcription or not the template? I'm confused about whether a sequence there that begins 5'-ATGGTGCGA-3' represents the template strand.

DR. CAROLYN:   This is in fact a difficult concept to fully understand. If the "ATG" in your example sequence represents a start codon, then you are looking at the coding (sense) strand, not the template (antisense) strand.

Double stranded DNA has a coding strand (which is also the + or sense strand) and a template strand (which is also the - or antisense strand). The transcription machinery actually reads the template strand. For your example sequence from GenBank, the coding strand is 5'-ATGGTGCGA-3' and the template strand is 3'-TACCACGCT-5'. The strand that can be computationally translated to derive the encoded protein sequence is the coding strand, 5'-ATGGTGCGA-3'. However, the cellular transcription machinery uses the template strand (i.e., 3'-TACCACGCT-5') to generate mRNA which can be translated to create a protein.


QUESTION FROM MARSHALL:   Is Chlamydomonas a plant or is it algae?

DR. CAROLYN:   Chlamydomonas is a a member of the lineage that gave rise to multicellular green plants. The kingdom to which Chlamydomonas belongs is in fact Viridiplantae (the green plant kingdom), but chlamy is also a unicellular alga. The group of organisms called algae is an assemblage of protists and plants that are simple, but they are not necessarily all related by descent.


QUESTION FROM JOHN:   I'm doing a leaf collection for trees, and we're supposed to label the leaves as coniferous or deciduous. One of the leaves I collected was from a tree called ginkgo. How should I label that leaf?

DR. CAROLYN:   What an excellent question! The answer is both! (Or neither, or something in between...) Webster defines the term deciduous as an adjective meaning, "falling off or shed seasonally or at a certain stage of development in the life cycle." Gingkos shed their leaves each Fall, so your leaf definitely can be labeled as having come from a "deciduous" tree.

However, in the past Ginkgo was classified as a conifer because it shared a lot of characteristics with coniferous species. For example, while flowering plants have no flagellated cells during any stage of their life cycle, conifers, Ginkgo, and other gymnosperms have flagellated, motile sperm. In addition, Ginkgo's reproductive structures often are referred to as cones. Presently Ginkgo is classified as the only member of the Ginkgophyta, a group distinct from both flowering plants (Magnoliophyta) and conifers (Coniferophyta). Ginkgo is definitely deciduous, and you could also defend calling it coniferous!


QUESTION FROM KIRI:   What's a mutation screen and a library screen, and why and how are they used?

DR. CAROLYN:   A 'mutation screen' is a process that is carried out to determine whether a given individual has a mutated copy of a gene or of some member of a suite of genes known to confer a given phenotype. For instance, if a researcher were screening a population of plants to determine whether any might be predisposed to heat shock sensitivity, she would first sequence genes known to be differentially regulated during heat shock conditions in wild type plants. Next she would sequence those same genes in plants known to be sensitive to heat shock to determine which genes might cause heat shock sensitivity if mutated. With this information, she could carry out a mutation screen aimed at identifying plants with an elevated risk of demonstrating heat shock sensitivity: those with the wild type sequences would not be considered to be at risk for heat shock sensitivity whereas those with sequences that were different than wild type or that matched the sequences belonging to plants that were heat shock sensitive would be tagged as at risk individuals.

A 'library screen' is a process used to find a specific cloned piece of DNA among a lot of other cloned DNA fragments... It's a way for researchers find the proverbial needle in a haystack. For example, if a researcher were interested in finding a cloned, full length sequence for a given gene and already had a fragment of the gene in hand, she could screen colonies of bacteria carrying plasmids of cloned DNA using the known gene fragment as a probe. Those colonies bearing DNA that the probe interacted with would be isolated, cultured, and sequenced to confirm whether they carried plasmids containing the full length gene.

As you can see, these two screening protocols are similar in that they are both designed to identifiy individuals of interest among a large population, but they address different biological problems: a mutant screen identifies organisms that are predisposed to developing some given phenotype whereas a library screen identifies cloned DNA of interest among a sea of non-matching DNA.


QUESTION FROM EUGENE:   What sorts of plants are behind you in the Ask Dr. Carolyn picture above?

DR. CAROLYN:   The picture was taken at the Grosser Garten in Dresden, Germany. The plant just in front of me in that picture is of a member of the palm family, Arecaceae. However, until consulting with Andy Tull at the University of Georgia, I didn't know the name of the plant you're asking about! Andy says that it is an member of the genus Aristolochia, which is considered to be a basal angiosperm. The inflated base of the plant's flower is a flytrap: flies are attracted by the flower's musky odor and serve as pollinators. These plants are sometimes called calico flowers or Dutchmen's pipe.


QUESTION FROM XIAO:   What is the difference between homologous chromosomes and sister chromatids?

DR. CAROLYN:   Sister chromatids are attached to each other at the centromere. Together two sister chromatids constitute a chromosome. In diploid organisms like flowering plants and human beings, there are two copies of each chromosome present in the genome, one from the organism's male parent and one from the female parent. Chromosome one from the female parent is homologous to chromosome one from the male parent. Each copy of chromosome one is then made up of two sister chromatids.


QUESTION FROM RONALD:   I keep seeing a term used that I'm not sure about: it appears that researchers are using the word "metazoans" as a descriptor for the group of all organisms that are multicellular. Is this a correct usage of that word?

DR. CAROLYN:   No, it's not. Actually, the term "metazoa" is a synonym for the kingdom name animalia. The plant kingdom's analogous term is "metaphyta." To refer to all multicellular organisms as a group, I suggest you do just that! Call them "multicellular organisms."


QUESTION FROM BEN:   What is an overgo and how do I create/use one? My major professor suggested I use overgos to probe for miRNAs, but I can't find a good explanation and protocol to evaluate and possibly try out!

DR. CAROLYN:   Please read the MaizeGDB overgo description for the general public, which can be found here. Another good description of overgos and a protocol describing how to use them can be found here. Good luck with your work, Ben!


QUESTION FROM EVIE:   How can I find out the exact Latin name for sunflowers?

DR. CAROLYN:   There are lots of ways to determine the botanical (Latin) name for a given species. I usually use online resources and recommend browsing the Arizona Tree of Live project (http://tolweb.org/tree/phylogeny.html) or trying out NCBI's Taxonomy Browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Using the Taxonomy Browser, I found this page which lists the full taxonomic classification of the common sunflower (Helianthus anuus).


QUESTION FROM JIMMY:   Do plants have chromosomes that make them be male or female?

DR. CAROLYN:   Very few plants have special chromosomes that determine sex, and those that do are not always evolutionarily closely related. For this reason, it is thought that the ancestors of flowering plants were hermaphroditic, which is to say that they had both male and female structures on the same plant or even within the same flower.

When a plant has both male and female structures present within the same flower, that flower is termed ‘complete.’ When a flower has only male OR female structures, that flower is termed ‘ incomplete.’ If the flowers are incomplete but both types of flowers are borne on a single plant, the plant is said to be monoecious. Sometimes a single plant has only male OR female flowers, with the other gender represented on other individuals. Such plants are called dioecious. Only plants that are dioecious have apparent sex chromosomes, and not all dioecious plants have them.


QUESTION FROM CONRAD:   Which animals hibernate? Are they evolutionarily closely related? Are the molecular processes involved in this known, and if so, are there similar processes in plants as they prepare for winter?

DR. CAROLYN:   Biologists disagree on what the word hibernation really means. Is it a specific sort of torpor or is it simply a term to be used for an extended deep sleep or a long period of inactivity? Using a loose interpretation of the word, MANY animals hibernate including bears, bats, frogs, and snakes. Invertebrates such as wasps, true bugs, and leaf beetles also hibernate. Since the distribution of hibernating animals spans the invertebrate/vertebrate divide, it is apparent that those animals that hibernate are not closely related in an evolutionary sense.

Certain aspects of the molecular processes involved in animal hibernation are known. One hibernation cue shared among many animals is shortening day length. Such a trigger causes signal molecules to be synthesized within the animal's cells (such as the gene product Hibernation Induction Trigger, HIT). Signal molecules like HIT induce the drop in body temperature and in metabolic rate that are hallmarks of hibernation initiation.

Plants can be thought to 'hibernate' during certain life stages. Trees lose their leaves during Fall, drawing important nutrients and sugars out of the leaves before they are detached. Throughout Winter they engage in little to no growth, and their metabolism slows. In the Spring, those nutrients and sugars that have been stored in the roots are sent back out to limbs where new leaves are initiated and the period of metabolic activity can begin anew.

Another period that could be considered to be a sort of plant hibernation is the period during which a seed waits to germinate before becoming a plant. Most animals reproduce in such a manner that young hatch or are born from the parent directly. Gymnosperms (like pine trees) and angiosperms (flowering plants) produce seeds that can exist for an extended period of time before germinating... Even for decades or centuries in some cases! This period of metabolic inactivity could be considered to be another instance of 'hibernation' during the life cycle of a plant.

What do animal and plant hibernation have in common? They are both brought on by environmental cues, most often daylength, and they are marked by a period of metabolic inactivity.


QUESTION FROM BING:   What does EST stand for? How many ESTs can a plant have? Which plant has the most ESTs?

DR. CAROLYN:   'EST' is an acronym for Expressed Sequence Tag. Within the genome there are stretches of DNA that encode genes. These regions are transcribed as messenger RNAs (mRNAs), and those mRNAs can be complemented by DNA in the laboratory. One or both ends of a complementary DNA (cDNA) can serve as the tag for sequencing, and the resulting sequence is referred to as an EST. Because any one gene's mRNA transcripts can be complemented and sequenced in the laboratory many times, the number of possible ESTs from a given organism is astronomically high (which is to say, one gene can yield many ESTs). For that reason, there is no definitive numerical answer to your question, "How many ESTs can a plant have?" At the National Center for Biotechnology Information (NCBI), the number of publicly available sequenced ESTs is reported by organism (click here). As of November 21st of 2003, Triticum aestivum (wheat) is the plant that has the largest number of available ESTs. Other plants with large numbers of ESTs available are Zea mays (maize or corn), Hordeum vulgare ssp. vulgare (barley), and Glycine max (soybean).


QUESTION FROM TIM:   Which plants have the largest genomes?

DR. CAROLYN:   The amount of DNA in the nucleus of an organism is called its C-value. Of those plants with known C-values, the ones with the highest values (hence the most DNA) are lilies. The plant that currently holds the record for highest C-value is Fritillaria assyriaca. Alium species (onions) also have high C-values.


QUESTION FROM EMILY:   We learned in class that plant sediments called peat were turned into coal, oil or petroleum, and natural gas by millions of years of pressure. If plants are still growing and dying and their remains are still being exposed to pressure, why are petroleum products considered to be non-renewable resources?

DR. CAROLYN:   When plants first came on the scene, no organisms relied upon them yet for food. Plant remains sank to the bottom of swamps where millions of years of pressure turned them into petroleum products. Since that time, organisms began to consume plants, breaking down plant remains into small molecules. Because plant remains are assimilated into other organisms before they can sink to the depths of swamps to be crushed by pressure, no petroleum is being generated at present. The short answer to your question, then, is that the process of evolution is the reason that petroleum products are non-renewable resources!


QUESTION FROM DAVID:   Why don't plants use centrioles as spindle poles during mitosis?

DR. CAROLYN:   Some plants DO use centrioles as microtubule organizing centers for mitosis. Included in this group are mosses, ferns, and gymnosperms. The group of plants that do not use centrioles are the angiosperms or flowering plants. Because flowering plants evolved from plants that did use centrioles to nucleate microtubules for spindle formation, it is thought that the ability to form centrioles was lost over the course of evolution. Flowering plants don't use centrioles as spindle poles during mitosis because they simply don't have them to use! Although many programs are currently trying to find out exactly how plants are able to organize their spindles in the absence of centrioles, a clear understanding of this process is still lacking.