One of the questions we often ask about forests is simply, “What’s out there?” What species are growing there? What does the forest look like visually? Are the trees young, old, or mixed? What is the proportion of small to large trees? Is there a tree canopy with a shrub layer underneath? Is the understory mainly herbaceous plants? Are there several layers of trees? Are snags or large fallen logs present? How dense is the forest? Do the trees have ample room to grow or are they crowded together? Forests display a vast array of species and structural arrangements (Figure 5.1.)
Figure 5.1. Examples of various forest stand structures.
A common task of the forest technician is to provide data to answer these questions. A survey called a “stand exam” is just that – an examination of the composition and structure of the forest. Once an assessment of the current conditions is completed, then questions about “What’s happening out there?” or “What will the stand look like in the future?” can be addressed more readily.
Stand Structure refers to the overall “look” of the forest stand (Figure 5.1). It is the “horizontal and vertical distribution of components of a stand, including the height, diameter, crown layers and stems of trees, shrubs, herbaceous understory, snags and down woody debris” (Helms 1998).
As one might imagine, the structure of a forest changes over time, as trees grow, as fungi rot the wood, as insects or fire move through, as light conditions change, and so on. Therefore, a stand exam is always a measure of the forest at a point in time; a snapshot, not a hard and fast truism. To successfully manage for wildlife habitat, wood quality, desired growth rates and a myriad of other forest management objectives, foresters often a) assess what is present, b) describe what is desired in the future, then c) develop guidelines for managing toward that future forest structure. We can’t wave a magic wand and proclaim, “Increase photosynthesis,” or “Speed up nutrient cycling,” so our current tools for influencing forest function center on influencing a forest’s species composition and structural elements.
Figure 5.2. Tree density illustrates the horizontal distribution of trees. The top photo shows a dense forest with many trees (or stems) per acre. The lower photo is less dense, with fewer trees per acre.
Let’s look at that stand structure definition again. “…horizontal and vertical distribution of components of a stand…..crown layers…” What terms can we use to adequately but briefly describe “distribution?” Horizontal distribution can be expressed in measures of density – trees per acre or basal area per acre (Figure 5.2). The crown is the foliar portion of the plant, and “crown layers” refers to distinct classes or stratification of the canopy. Since trees dominate the canopy of most forests, several forestry terms describe the vertical distribution, or layering of the tree crowns.
An evenaged forest is has one or two distinct age or size classes of trees; thus one or two layers of tree crowns(Figure 5.3A).
Figure 5.3A. Evenaged forests: a single layered canopy (left) and a two-aged stand (right).
An unevenaged forest has three or more distinct age or size classes, thus three or more layers of trees (Figure 5.3B).
Figure 5.3B. A multilayered unevenaged stand, with three or more cohorts.
Although it is common to have a canopy of trees overhead, shrubs at midstory, and herbs on the forest floor, we would not refer to this as unevenaged unless there are several layers of trees. A multistoried stand is one with multiple layers of trees. As we learned before, tree size does not always indicate tree age; therefore, some foresters try to avoid the terms “evenaged,” “unevenaged” and “age classes,” and instead refer to forest “size classes” or “cohorts” to describe the distinct tree layers of a forest. So when you read “evenaged” think “one dominant layer in the overstory.” When you read “unevenaged” think “three or more tree layers.”
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Living Systems are organized in a hierarchy of structural levels that interact.
Explain how a change in the subunits of a polymer may lead to changes in structure or function of the macromolecule.
Directionality of the subcomponents influences structure and function of the polymer –
- Nucleic acids have a linear sequence of nucleotides that have ends, defined by the 3’ hydroxyl and 5’ phosphates of the sugar in the nucleotide. During DNA and RNA synthesis, nucleotides are added to the 3’ end of the growing strand, resulting in the formation of a covalent bond between nucleotides.
- DNA is structured as an antiparallel double helix, with each strand running in the opposite 5’ to 3’ orientation. Adenine nucleotides pair with thymine nucleotides via two hydrogen bonds. Cytosine nucleotides pair with guanine nucleotides by three hydrogen bonds.
- Proteins comprise linear chains of amino acids, connected by the formation of covalent bonds at the carboxyl terminus of the growing peptide chain.
- Proteins have primary structure determined by the sequence order of their constituent amino acids, secondary structure that arises through local folding of the amino acid chain into elements such as alpha-helices and beta-sheets, tertiary structure that is the overall three-dimensional shape of the protein and often minimizes free energy, and quaternary structure that arises from interactions between multiple polypeptide units. The four elements of protein structure determine the function of a protein.
- Carbohydrates comprise linear chains of sugar monomers connected by covalent bonds. Carbohydrate polymers may be linear or branched.
A Structure-based QSAR and Docking Study on Imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4,]benzodiazepines as Selective GABAAα5 Inverse Agonists
As three-dimensional (3D) structure of the GABAAα5 was not determined, the crystal structure of 2Vl0E at 3.3 Å resolution which is a ligand-gated K + channel was used as a template in homology modeling, and the result was used in molecular dynamic simulation for obtaining its conformation in a water sphere. The resulted conformation of the receptor was used for docking with the most potent of imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4,] benzodiazepines drugs to find out binding sites and consequently the types of the interaction between the drugs and receptor. The results showed that π–π interaction of the drugs with three phenylalanine and tyrosine residues plays an important role in determining the potency of the inhibitors. The obtained information relating to the binding sites of the receptor was utilized for docking all the drugs into the receptor and find out optimized conformation for each drug, used in structure-based quantitative structure-activity relationship (QSAR) model for calculation of descriptors. Then, selected descriptors were related to the binding affinity and selectivity of the drugs using multiple linear regression and least squares-support vector regression. Finally, the results of target- and ligand-based QSAR models were compared, resulted the superiority of the structure-based QSAR to the ligand-based model.
Appendix S1. The homology model of GABAA α5 obtained from SWISS-MODEL server in a text format.
|CBDD_1183_sm_AppendixS1.txt232.3 KB||Supporting info item|
|CBDD_1183_sm_AppendixS1.pdb232.5 KB||Supporting info item|
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