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7.4: Types of Root Systems - Biology

7.4: Types of Root Systems - Biology


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Plants that have adapted to different environments might develop different root systems in response to the stressors in that environment. Observe the different root systems available in lab and try to classify them as one or more of the following:

Netted or Taproot System

In soils where water is readily available for most of the year, plants might develop a netted root system where many similar diameter roots capture as much water and nutrients as possible to outcompete their neighbors. In climates where there are droughts or freezes, plants might develop a taproot system, where a larger central root can burrow deeper into the soil profile, accessing water reserves that other plants cannot.

Storage Roots

A larger diameter root can also store water and/or sugars for long periods. This type of root is called a storage root. A large central root, such as in the middle left on the following page, could be both a taproot and a storage root.

Adventitious Roots

Adventitious roots emerge from stem tissue. This can happen when there is an underground stem, such as in the system at the top of the diagram on the following page, or to serve as a prop root, as in the center of the diagram.

In the figure above, label any adventitious roots, prop roots, and storage roots. Label each system as either netted or taproot (except the topmost root system, which is an underground stem).


Anatomy and Physiology: Types of Joints

Any place where two bones meet is called an articulation (or joint). It might help you to remember that a person is articulate when she/he can string words together (making joints!) well. Don't forget that bones are used for more than movement, so the range of motion is going to vary a great deal, with the least amount of motion in those bones that are mainly for protection. There are two basic ways to classify joints (as seen in the following table): by virtue of structure and by virtue of function. (There's that structure and function duality again!)

Classification of Joints
Joint Type Characteristics Location
Structural Classification
Fibrous No joint cavity, held by fibrous connective tissue Skull sutures, tooth and mandible
Cartilaginous No joint cavity, held by cartilage Pubic symphysis, epiphyseal plate
Synovial Joint cavity, bones are surrounded by articular capsule, and often accessory ligaments Knee, elbow, phalanges, and so on
Functional Classification
Synarthrosis Immovable joint Skull sutures, tooth and mandible, epiphyseal plate
Amphiarthrosis Slightly movable joint Pubic symphysis, tibia-fibula (distal end)
Diarthrosis Freely movable* joint Knee, elbow, phalanges, and so on

*Diarthrosis joints are ?freely movable,? because they can move freely, but only within a limited range of motion based on the type of diarthrosis.

I Can't Move!

We have all learned so well that bones help us to move (which explains why some texts refer to a musculoskeletal system) that we forget how often bones are used for simple structural support and protection. One very useful way to accomplish these functions is to be immobile. There are three types of immobile joints in the body. Sutures in the skull are one example their principal function is to protect the brain. These fibrous joints, which form as the skull develops, resemble the meandering pattern of a river, and their pattern is unique in every skull. Remember the fontanels from the last section? Fontanels, which are basically preossified sutures, enable the skull to be flexible during delivery.

A gomphosis is a peg-and-socket joint. This type of joint makes perfect sense when you consider your teeth. The root of each tooth is the peg shape, and in both the inferior surface of the maxilla and the superior surface of the mandible, there is a line of sockets for each of the teeth. At the tip of the root there is a periodontal ligament that connects the root to the jaw, which is what makes pulling teeth so difficult.

Lastly, a synchondrosis is an example of a joint where you don't think a joint would be, simply because it is within the bone. As I mentioned in The Bones, at the epiphysis of every long bone is an epiphyseal plate of hyaline cartilage where the bone growth occurs, at least until adulthood when it ossifies (turns to bone), at which point it is called a synostosis.

A Little Wiggle Room

There are two types of slightly movable joints (amphiarthrosis): syndesmosis and symphysis. A syndesmosis is similar to a suture, complete with the fibrous connective tissue, but it is more flexible. Such a joint is useful if the body needs to link two bones, but allow a little flexibility. A perfect example can be found between the tibia and the fibula. The proximal joint involves only those two bones, but the distal end of each bone also articulates with the talus, which is part of the ankle. The joint between the tibia and fibula thus needs to be both rigid and flexible.

The other amphiarthrosis is called the symphysis, and it is characterized by a broad, flat piece of fibrocartilage, which both cushions the joint and allows some movement. There are two examples of this in the body: the intervertebral disks and the pubic symphysis. The intervertebral disks wear down and flatten over time, which is one of the reasons why people get shorter when they age! The pubic symphysis is the only place where the two pelvic bones articulate (the other articulations are with the femur and the sacrum). This joint is loosened by the hormone relaxin during the ninth month of pregnancy, which eases delivery.

Make Room!

Medical Records

With all these terms ending in -arthrosis, is it any wonder that an inflammation of a joint is called arthritis? There are many forms of arthritis, with a wide variety of causes. Perhaps the most debilitating is osteoarthritis, in which the cartilaginous parts of the joint actually ossify (turn into bone), thus permanently eliminating movement in that joint.

A diarthrosis is also called a synovial joint, named after the structures that make them so freely movable. The defining characteristic of a synovial joint is what is called the synovial joint cavity, filled with synovial fluid, which separates the bones in the joint. This cavity, and the structures in and around it, are more complex than other joints, but they are necessary in terms of providing so much motion.

Medical Records

Have you ever heard people crack their knuckles and wondered what that gross sound was? By pulling on a knuckle you increase the volume of the cavity, thus decreasing the pressure (see Boyle's law in The Digestive System) this can cause some of the synovial fluid to evaporate, and thus make a bubble. When the pressure in the capsule exceeds that in the bubble, the bubble implodes?thus the pop! Any small bubbles left need to fully dissolve before the joint can be cracked again (23 to 30 minutes).

At the end of each articulating bone is a cap of hyaline cartilage called articular cartilage, which serves to protect the bones, but does not connect the two bones. You might remember having seen it the last time you ate a chicken leg. Around the joint as a whole is an articular capsule, which encases the synovial joint cavity. The articular capsule has two layers: a tough outer layer called the fibrous capsule and an inner synovial membrane.

The fibrous capsule, which is made of dense, irregular connective tissue, has two distinct functions. One is to provide enough flexibility to allow movement, and the other is to provide enough strength to prevent dislocating the joint. The greater the flexibility in a joint, the easier it is to dislocate the joint. The ball-and-socket joint allows the greatest range of motion, but the shoulder has far more flexibility than the hip. This is presumably related to our evolutionary past, in terms of needing the pelvis to provide adequate support for our bipedal nature, and a holdout of our ancestors' heavy use of brachiation (arm over arm swinging?think monkey bars). As such, it is understandable that the shoulders get dislocated far more often than the hips.

The inner synovial membrane is a bit of a mish-mash, with areolar connective tissue, adipose tissue, and some epithelial tissue with the cells uncharacteristically widely spaced. This membrane secretes a viscous synovial fluid the consistency of raw egg white that lubricates the joint. Wear and tear on the joint is also cleaned up via macrophages in the fluid. Lastly, since cartilage is avascular, the fluid aids in the distribution of nutrients to the cartilage around the joint.

Most synovial joints also have accessory ligaments. Ligaments outside the capsule are called extracapsular ligaments, with those inside the capsule called intracapsular ligaments. A joint with a lot of use will also have a pad of fibrocartilage called an articular disk, which is also called a meniscus. All of this motion might also cause a lot of friction against the muscle and skin. An extra measure of protection are the bursa, which are similar to articular capsules, complete with fluid, but without the bones. When these capsules get inflamed, that condition is known as bursitis.

Excerpted from The Complete Idiot's Guide to Anatomy and Physiology 2004 by Michael J. Vieira Lazaroff. All rights reserved including the right of reproduction in whole or in part in any form. Used by arrangement with Alpha Books, a member of Penguin Group (USA) Inc.


Tree Root Systems

Tree roots serve a variety of functions for the tree. Roots absorb and transfer moisture and minerals as well as provide support for the above ground portion. There are two basic types of roots, woody and nonwoody.

Nonwoody roots are found mostly in the upper few inches of soil. The primary function of these roots is to absorb water and nutrients. These are often called feeder roots. In addition, some trees, particularly deciduous trees such as ash, have extensions called root hairs which increase root surface area and increase nutrient and water uptake. Evergreen trees such as pine may not have root hairs but possess mychorrhizae. Mychorrhizae are fungi which live on and in the feeder roots. This fungi do not cause any harm to the tree. In fact, for some species it is very beneficial for the tree to have this fungal association.

Woody roots are large lateral roots which form near the base of root and stem (the root collar). The primary purpose of these roots is support and anchorage for the tree. They also provide water and mineral transport as well as carbohydrate storage. These roots are distinct for each tree species and provide the framework for the tree's root system. The general direction for this framework is radial and horizontal. These roots are located 8 to 12 inches below the soil surface and can extend 4 to 7 times the drip line of the tree. These roots are perennial and show annual growth rings, which is why many tree roots eventually become exposed.

In drier soils, some tree species will form "striker roots" at intervals along the framework system. These roots grow vertically downward until they encounter an obstacle or soil with insufficient oxygen for growth. They will often branch and form a second layer of roots deeper in the soil. These roots function as water and food storage areas for the tree.

Another type of root is the adventitious root. These roots will often form spontaneously at the root collar from large woody roots. Although it is not known exactly what causes their formation, they usually develop as a result of injury.

There are many misconceptions about root growth in trees. Horizontal root spread is one of the more important. It is often said that the majority of feeder roots are concentrated at the dripline of the tree. Roots extend to that distance and much farther. Studies have shown root spread to be 4 to 7 times the dripline distance (radius) of the tree. This is an important fact to remember when applying herbicides, fertilizers, insecticides, and other soil treatments around trees. Careful consideration can prevent serious injury to your trees.

Another misconception is root depth. Roots will grow wherever the environment is favorable. They require water, oxygen, minerals, support, and warmth. These requirements are usually found in the upper few feet of soil. Roots rarely grow below four feet although there are numerous cases stating the opposite. The major portion of a tree's root system is in the top few inches of soil. This makes it easier to understand why trees can be easily uplifted during wind storms or other soil disturbances.

The main point to take home from this is that tree roots are extensive and are located in the upper few inches of soil. Broadcast fertilizers are very much available to the tree roots as are herbicides and other chemicals. Soil compaction is one of the biggest problems a tree root can have. Water and oxygen become unavailable when the pore spaces are closed. Avoid large grade changes during construction, both filling and removal. Avoid the use of plastic as a mulch or under mulches, use weed barriers that breathe. Many tree problems are accidental, by understanding more about the tree root system, these problems can be avoided.

This article originally appeared in the April 1, 1992 issue, pp. 1992 issue, pp. 43-44.


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4 Types of Dental Bridges

If you’re a prime candidate for this type of restoration, your next step will be to educate yourself on the types of dental bridges. Considering the American Dental Association estimates that most adults are missing three teeth, it’s possible you may even need more than one!

Knowing the options available to you will help you understand your dentist’s recommendations and determine which of the types of bridges is the best choice for you.

1. Traditional Bridge

As you can assume, traditional bridges are the most historically popular choice. The pontic is held in place by dental crowns placed on the natural teeth on both sides of the gap.

This is a very strong type of bridge, and can even replace a molar.

One downside is that your dentist will need to remove enamel on these adjacent teeth in order to secure the crowns.

Enamel doesn’t grow back once totally removed, so the decision to get these crowns is a permanent one. Even if you decide on a different treatment option later, these abutments will need crowns for the rest of your life.

Getting a traditional bridge is not a decision to take lightly.

2. Cantilever Bridge

A cantilever bridge differs from a traditional bridge in that the pontic, or false tooth, is only supported on one side of the gap. These are typically needed when there is more than one missing tooth adjacent to each other.

Unfortunately, this model can be less stable due to its single-sided support structure. It can lead to issues down the road, such as a loosened crown on the abutment or fractured teeth in the surrounding area.

3. Maryland Bridge

The Maryland bridge isn’t located in the northeast, but in the mouths of thousands of Americans. This conservative model has a pontic held in place by either porcelain or metal arm or wings (called the framework) surrounding the artificial tooth.

This dental bridge option is ideal for cases where the teeth haven’t finished growing, such as adolescent tooth loss. In most cases with a Maryland bridge, a more permanent bridge or even partial dentures will be used at a later date.

4. Implant-Supported Bridges

An implant-supported bridge is straightforwardly named: this bridge uses dental implants to support a bridge, usually in cases needing several artificial teeth.

This eliminates the need to use a crown on a natural tooth, and typically uses one implant per missing tooth. It’s not a good idea to use a bridge with just one implant for one tooth.

It’s an extremely strong and durable option, but an implant-supported bridge requires additional surgery to secure the implants into the jawbone.


Multiple factors limit plant growth

Fundamentally, plants require energy (light), water, carbon and mineral nutrients for growth. Abiotic stress is defined as environmental conditions that reduce growth and yield below optimum levels. Plant responses to abiotic stresses are dynamic and complex [8, 9] they are both elastic (reversible) and plastic (irreversible).

The plant responses to stress are dependent on the tissue or organ affected by the stress. For example, transcriptional responses to stress are tissue or cell specific in roots and are quite different depending on the stress involved [10]. In addition, the level and duration of stress (acute vs chronic) can have a significant effect on the complexity of the response [11, 12].

Water deficit inhibits plant growth by reducing water uptake into the expanding cells, and alters enzymatically the rheological properties of the cell wall for example, by the activity of ROS (reactive oxygen species) on cell wall enzymes [8]. In addition, water deficit alters the cell wall nonenzymatically for example, by the interaction of pectate and calcium [13]. Furthermore, water conductance to the expanding cells is affected by aquaporin activity and xylem embolism [14–17]. The initial growth inhibition by water deficit occurs prior to any inhibition of photosynthesis or respiration [18, 19].

The growth limitation is in part due to the fundamental nature of newly divided cells encasing the xylem in the growing zone [20, 21]. These cells act as a resistance to water flow to the expanding cells in the epidermis making it necessary for the plant to develop a larger water potential gradient. Growth is limited by the plant's ability to osmotically adjust or conduct water. The epidermal cells can increase the water potential gradient by osmotic adjustment, which may be largely supplied by solutes from the phloem. Such solutes are supplied by photosynthesis that is also supplying energy for growth and other metabolic functions in the plant. With long-term stress, photosynthesis declines due to stomatal limitations for CO2 uptake and increased photoinhibition from difficulties in dissipating excess light energy [12].

One of the earliest metabolic responses to abiotic stresses and the inhibition of growth is the inhibition of protein synthesis [22–25] and an increase in protein folding and processing [26]. Energy metabolism is affected as the stress becomes more severe (e.g. sugars, lipids and photosynthesis) [12, 27, 28]. Thus, there are gradual and complex changes in metabolism in response to stress.


Abstract

The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydropatterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 and PIN-FORMED 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root.

The root system of plants is a branched network whose architecture is determined by endogenous and environmental cues and serves as a model for pattern formation (1). In Arabidopsis, lateral roots (LRs) are initially specified as founder cells (FCs) within the internal pericycle cell layer of the primary root (2). A temporally oscillating transcriptional network that results in periodic fluctuations in auxin response controls the patterning of FCs along the longitudinal axis of the primary root (3, 4). Moments of peak auxin response are maintained in fixed positions termed prebranch sites (PBS), which mark presumptive FCs and can be visualized using the ProDR5:LUC+ reporter (4). In Arabidopsis, LRs only develop from pericycle cells that overlie one of the two xylem poles (5). Although two such populations of cells exist along the circumferential axis of the root, pericycle cells adjacent to only one xylem pole will be selected. How the xylem pole is chosen and whether environmental stimuli affect this process is currently unclear.

We report that when roots are grown vertically on the surface of an agar medium, LRs predominantly form on the side of the primary root that contacts agar. Through our developmental analysis, we show that the local environment impacts LR patterning by providing spatial cues that select one of the two xylem poles at which LR FCs will be specified. We observe this patterning phenomenon in all flowering plant species examined and also in a realistic soil environment. Because this phenomenon is elicited by exposing roots to an asymmetric distribution of available water, we have termed the process “hydropatterning.”


New visualization and query capabilities

Visualization tools for individual biological entities

Genes/proteins/RNAs: Since our last publication [ 1 ], we merged the individual display pages for a gene and its product (protein or RNA) into a single page that combines all information in one central place. These pages are quite extensive, listing information such as the map position of the gene on the chromosome, a graphical depiction of the chromosomal region containing the gene and available gene-essentiality information. A new diagram, the regulation-summary diagram, integrates all known regulatory influences on the gene and gene product into a single figure. Common to all protein types is the ability to graphically display information about protein regions (such as phosphorylation sites and active sites) using a protein-feature ontology that we developed.

Pathways: We recently added the ability to display gene expression and metabolomics data on pathway diagrams (see Figure 2 ). Support for display of signaling pathways (see Figure 1 ) was added recently signaling pathway layout is performed by the user.

The EcoCyc L-ornithine biosynthesis pathway shown with omics pop-ups containing time-series data from a gene-expression experiment.

The EcoCyc L-ornithine biosynthesis pathway shown with omics pop-ups containing time-series data from a gene-expression experiment.

Electron transfer reactions and pathways: A crucial role in cellular metabolism is played by electron transfer reactions (ETRs), which are of key importance in the energy household of a cell. In a series of redox steps, the high-energy electrons from some compounds drive the pumping of protons across a cell membrane, to maintain the proton motive force needed for ATP synthesis. We designed and implemented drawing code for a special ETR diagram, which shows the enzyme complex embedded in a membrane, and which schematically depicts the flow of electrons from one redox half reaction to another. Inside the membrane, the quinone/quinol cofactor is shown together with an indication of the cell compartments that are sources or sinks of the protons. An additional vectorial proton transport reaction can be added to the diagram. This results in displaying the flow of all substrates and products relative to the cellular compartments, in a similar way to what is customary in the biomedical literature. Pathways consisting of several ETRs joined together can also be depicted (see Figure 3 ).

An electron transfer pathway diagram.

An electron transfer pathway diagram.

SmartTables: large-scale manipulation of PGDB object groups

SmartTables is a recent addition to Pathway Tools, which enables users to construct and manipulate groups of PGDB objects through a spreadsheet-like user interface [ 19 ] (SmartTables were previously called Web Groups). SmartTables provide many powerful operations to biologist end users that previously would have required assistance from a programmer, and our user surveys indicated that SmartTables are reasonably easy for biologists to use [ 19 ]. Altogether, 2700 users of BioCyc.org have created more than 31 000 SmartTables.

A typical SmartTables use case is for a user to define a SmartTable by importing a list of PGDB objects from a file. For example, a user could define a metabolite SmartTable by importing a list of metabolites from a metabolomics experiment, where the metabolites are specified by metabolite name, BioCyc identifier, PubChem identifier or KEGG identifier. (The set of objects in a SmartTable can also be defined from a query result, from any column of an existing SmartTable, or from the set of, say, all genes in a PGDB.)

The user can browse the set of objects in a SmartTable by paging through the table, and can modify the information displayed about each object by specifying which table columns to include (see Figure 4 ). SmartTable columns are derived from the PGDB attributes available for each object, and can include information such as chemical structures, molecular weights, links to other DBs and nucleotide and protein sequence. A variety of filters and set manipulations are provided for SmartTables, such as removing or retaining all rows that match a user query, and computing the union, intersection and set difference of two SmartTables. SmartTables are stored in the user’s online web account, and a desktop version of SmartTables is also provided. SmartTables are private by default, but the user can make them public, share SmartTables with selected other users or archive them in a frozen form in conjunction with a publication.

A gene SmartTable. Column 1 shows the gene name, column 2 shows the E. coli genome ‘b-number' accession number for the gene (a property) column 3 shows the gene product name (a property). Column 4 shows the result of a transformation in which the regulator(s) of each gene were computed.

A gene SmartTable. Column 1 shows the gene name, column 2 shows the E. coli genome ‘b-number' accession number for the gene (a property) column 3 shows the gene product name (a property). Column 4 shows the result of a transformation in which the regulator(s) of each gene were computed.

Several more advanced SmartTable operations are provided. ‘Transformations' compute new columns from relationships in a PGDB. For example, column 4 in Figure 4 is a transformation column that shows one or more regulators for each gene in column 1 that has been computed from PGDB relationships. Other gene transformations available include computing the metabolic pathways in which a gene’s product occurs and computing the amino-acid changes caused by sequence variants. Different transformations are available for different datatypes. For example, the transformations available for a metabolite SmartTable include computing the reactions in which a metabolite occurs, the pathways in which a metabolite occurs, the proteins for which the metabolite is a ligand and mapping the compounds to their equivalents in another PGDB.

A user can perform a statistical enrichment analysis on a gene or metabolite SmartTable to detect overrepresented metabolic pathways or Gene Ontology (GO) terms, or overrepresented metabolic pathways, respectively. In addition, a SmartTable of genes or metabolites can be visualized on the cellular overview.

System-level visualization of metabolic networks

Pathway Tools can automatically generate organism-specific metabolic charts that we call Cellular Overview diagrams [ 2 ]. The diagram can be interrogated interactively and used to analyze omics data sets. Recently, the diagram was reengineered for the web mode of Pathway Tools. The diagram can be generated as a PDF file for printing as a large-format poster. Example posters can be downloaded from [ 20 ].

Figure 5 depicts the Web Cellular Overview at low resolution painted with gene-expression data. It contains all known metabolic pathways and transporters of an organism (online example: [ 21 ] example with animated display of omics data: [ 22 ]). Each node in the diagram represents a single metabolite, and each line represents a single bioreaction. Biosynthetic pathways are in the left half of the diagram catabolic pathways are in the right half.

The Pathway Tools Cellular Overview diagram for EcoCyc, painted with gene-expression data. Omics pop-ups are shown for two genes.

The Pathway Tools Cellular Overview diagram for EcoCyc, painted with gene-expression data. Omics pop-ups are shown for two genes.

Omics data (e.g. gene-expression or metabolomics measurements) for a given organism can be painted onto the cellular overview to place this data in a pathway context and to enable the user to discern the coordinated expression of entire pathways (such as the TCA cycle) or of important steps within a pathway. The user can click to create omics pop-ups that graph all available time points for particular reactions or metabolites of interest. Omics data may be loaded from a data file, from a GEO data set retrieved via web services or from a SmartTable. The data may be generated from a variety of experimental technologies, including microarrays and next-generation sequencing. Lower-level data processing must be performed external to Pathway Tools and must produce an expression value (or series of values) for each gene, protein, metabolite or reaction. The input data files can mix values for multiple types of entities such as genes and metabolites. Each entity can be specified using one or more names or identifiers to maximize the chances that Pathway Tools will recognize each entity. For more information on omics data file formats, see [ 23 ]. In web mode, the user has a choice of several color schemes—in desktop mode the color scheme is fully customizable.

Cellular Overview diagrams are generated automatically using an advanced layout algorithm [ 2 ]. Automated layout is essential to enable the diagram to accurately depict the underlying DB content as that content evolves, without requiring time-consuming manual updates by curators that are bound to overlook some updates. In addition, automated layout enables generation of organism-specific cellular overviews that reflect the exact pathway content of each organism-specific PGDB in large PGDB collections such as BioCyc.

The Cellular Overview has many capabilities (described in more detail in [ 2 ]), including semantic zooming of the diagram (where the highest magnification corresponds to the detail shown in the poster version) highlighting of user-requested elements of the diagram (such as metabolites or pathways) highlighting large, biologically relevant subnetworks (such as all reactions regulated by a given transcription factor) and highlighting comparative analysis results, such as comparison of the metabolic networks of two or more PGDBs.

System-level visualization of genome maps

The Pathway Tools genome browser displays a selected replicon (chromosome or plasmid), and enables the user to zoom into a region of the replicon by gene name or by coordinates. The browser supports semantic zooming: as the user moves deeper into the genome, additional features are displayed, such as promoters and terminators. The browser has been extended so that at high magnification, the genome sequence and the amino-acid sequence of coding regions become visible, and intron and exon boundaries are shown.

Sequence-based query and visualization tools

The following new tools support query and visualization of sequence data from a Pathway Tools web server.

Nucleotide Sequence Viewer: Gene pages include links to view or download the nucleotide or RNA/protein sequence for the gene. When viewing the nucleotide sequence, an option is provided to include an additional upstream and/or downstream flanking region of any desired length. This option makes it easy to, for example, view the sequence of a regulatory region surrounding a gene of interest. Alternatively, the user can enter specific start and end coordinates and the desired strand to view the sequence of any arbitrary portion of the chromosome.

Sequence Pattern Search (PatMatch): The PatMatch facility enables searching within a single genome for all occurrences of a specified short nucleotide or peptide sequence (less than about 20 residues), with the ability to specify degenerate positions. The user can specify the kind and number of allowable mismatches, and whether to search coding regions only, intergenic regions or the entire genome. Examples of situations in which this facility might be useful include searching for all occurrences of a particular regulatory motif upstream of any gene, or all occurrences of a known cofactor binding motif within proteins.

Multiple Sequence Alignment: From a gene page, users can request a multiple sequence alignment between the nucleotide or amino-acid sequences of that gene and its orthologs in a user-specified set of organisms. Alignments are displayed using MUSCLE [ 24 ].

Cross-organism search

We recently added a tool for searching across all organisms within a Pathway Tools web server, such as for the 5700 organisms at BioCyc.org. The cross-organism search tool [ 25 ] searches for user-specified combinations of words in the Common-Name/Synonyms attributes, and/or the Summary attribute. It can search all types of objects in a given PGDB, or in user-specified object types, such as genes and/or pathways. It can search all organism DBs present in the Pathway Tools web server, or it can search user-specified sets of organisms, such as all organisms within a selected taxonomic group. Indexing and searching is implemented using SOLR [ 26 ].


Non-endospermic seed structure (Eudicots): Fabaceae - pea as model system in seed biology

  • Non-endospermic seeds: The cotyledons serve as sole food storage organs. During embryo development the cotyledons absorb the food reserves from the endosperm. The endosperm is almost degraded in the mature seed and the embryo is enclosed by the testa. Examples: rape ( Brassica napus ), and the legume family including pea ( Pisum sativum ), garden or French bean ( Phaseolus vulgaris ), soybean ( Glycine max ).
  • Pea seeds: The embryo of mature seeds of Pisum sativum consists of the embryonic axis and the cotyledons. FA4-type seed. The fleshy storage cotyledons make up most of the seed's volume and weight. The pea embryo is enclosed by the testa and the endosperm is obliterated during seed development, when it's nutrients are taken up by the embryo. References on pea seed development: Marinos, Protoplasma 70: 261-279 (1970) and Hardman, Aust J Bot 24: 711-721 (1976).

Drawing of a mature pea (Pisum sativum) seed, a typical non-endospermic seed with storage cotyledons and the testa as sole covering letters. Color drawing published in Finch-Savage and Leubner-Metzger (2006).


Cover photograph of the May 2003 issue of Plant, Cell & Environment:
Germinated seeds of Pisum sativum showing the effect of ethylene on radicle growth. Seeds were
germinated (48 h) and then treated for 8 h with (left) or without (right) 30 µL / L ethylene
Petruzzelli et al., Plant Cell Environ 26: 661-671 (2003)

See the web page"Plant hormones" for information about ethylene and pea seed germination and seedling radicle growth.


Drought Tolerance

A deep taproot helps plants use moisture held in deeper soil layers, and they can have great drought resistance compared to fibrous-rooted plants. An example is honey mesquite (Prosopis juliflora), which is known to send its roots down 150 feet to get water. Fibrous roots near the surface of the soil, however, can take up water very quickly, helping plants such as saguaro (Carnegiea gigantea) glean water from even a light rainfall. Saguaros have both a deep taproot and a large fibrous root system. Honey mesquite, which has invasive tendencies, grows in USDA zones 9 through 11 and saguaro, in USDA zones 9a through 10b.

Carolyn Csanyi began writing in 1973, specializing in topics related to plants, insects and southwestern ecology. Her work has appeared in the "American Midland Naturalist" and Greenwood Press. Csanyi holds a Doctor of Philosophy in biology from the University of Wisconsin at Madison.