2_PHARM 104.1_BOTANICAL PHOTOGRAPHY .pdf

PHARM 104.1: PHARMACOGNOSY LAB BOTANICAL PHOTOGRAPHY Professor Jeffrey Mancera OUTLINE WHAT IS TAXONOMY?review 4 MAJOR STEPS OF TAXONOMY DESCRIPTION IDENTIFICATION NOMENCLATUREreview CLASSIFICATIONreview REVIEW OF PLANT MORPHOLOGYreview WHY PHOTOGRAPH PLANTS? DOCUMENTATION OF LIFE 6 ESSENTIAL ELEMEN...

PHARM 104.1: PHARMACOGNOSY LAB BOTANICAL PHOTOGRAPHY Professor Jeffrey Mancera OUTLINE WHAT IS TAXONOMY?review 4 MAJOR STEPS OF TAXONOMY DESCRIPTION IDENTIFICATION NOMENCLATUREreview CLASSIFICATIONreview REVIEW OF PLANT MORPHOLOGYreview WHY PHOTOGRAPH PLANTS? DOCUMENTATION OF LIFE 6 ESSENTIAL ELEMENTS IN TAKING QUALITY PLANT PHOTOS SCIENCE AND ART WHAT KINDS OF PLANT PHOTOS CAN WE TAKE? DEPENDS TO ITS SCALE MACROPHOTOGRAPHY EQUIPMENT COMPOSITION DIAGNOSTIC FEATURES OF A PLANT (IDEALLY THE) GENERAL FEATURES OF ANY PLANT TAXONS THAT HAVE SPECIFIC FEATURES LIGHT AND COLOR FOCUS AND EXPOSURE ACCESSORIES CONSIDERATIONS PHOTOMICROGRAPHY EQUIPMENT COMPOSITION LIGHT AND COLOR FOCUS AND EXPOSURE ACCESSORIES CONSIDERATIONS SUMMARY OF MACROPHOTOGRAPHY AND PHOTOMICROGRAPHY OPEN-FORUM PORTION link to Botanical Photography Lecture: Botanical Photography Lecture Recording - October 22, … WHAT IS TAXONOMY?review The study of classification that is widely used in many areas of knowledge. ○ sorting of things into some type of order ○ applicable to all intellectual endeavors in all fields 1. 2. 3. 4. In terms of Biology, Taxonomy is considered to be a specific branch that encompasses the description, identification, nomenclature, and classification of organisms, specifically living things. 4 MAJOR STEPS OF TAXONOMY Description* Identification* Nomenclature Classification *in botanical photography, these two are mostly we’re concerned with DESCRIPTION Assignment of features to a taxon We describe the features by assigning to things ○ Character attributes, traits leaf margin, vessel element, secondary wall, thickening ○ Character states two or more forms of a character entire, serrate, dentate, crenate, annular, spiral, scalariform, reticulate 🔊 🔊 🔊 🔊 IDENTIFICATION Associating an unknown taxon with a known one Dichotomous Keys ○ Consists of a series of two contrasting elements Lead ○ Single statement Couplet ○ Pair of leads, often contrasting Photograph plants the way you would describe them NOMENCLATUREreview Naming a taxon according to a standardized system Giving a taxon a formal name For plants, we have a rich set of rules and regulations that govern naming of plants Rules and regulation: ○ International Code of Nomenclature for algae, fungi, and plants ○ Mostly fixed international code, most rules and regulations have been effective for many years, but are still open to changes ○ Changes are strengthened especially if approved by big international botanical community ○ Every 6 years, rules and regulations are updated by botanists around the world, made during the International Botanical Congress. Fundamental Principle: ○ One taxon, one name – for every group of plants, there can only be one name. ○ For universality, assigning names is performed in a fixed language. ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK 1 ○ Names assigned are called SCIENTIFIC NAME, and are always in Latin. Therefore, Latin rules are followed. 1. Node - junction of the stem, it is also where axillary buds are found called stipules. 2. Stipules - leaf-like structures SCIENTIFIC NAME Family name - one word - non italicized - begins with a capital letter - ends with -aceae (e.g., Fabaceae) Genus name - specific group of plants within the family - one word - italicized when printed - underscored when handwritten - begins with a capital letter, with various endings (e.g., Pterocarpus or Pterocarpus) Species name 3. Flower a. sepals- leaf-like structure of a flower b. petals- colorful structures c. androecium -male structures i. anther - organ that produces the pollens ii. stamens - stalk d. gynoecium -female structures i. stigma - receives the pollen, tip of gynoecium ii. style -stalk iii. ovary - produces ovules placentation- attachment ○ ovules - become seeds - there may be different species within a genus - more specific than family and genus - comprised of two words: genus and specific epithet (binomial) - italicized - specific epithet does not begin with a capital letter - ends with various suffixes, usually similar to the genus name Figure 1. Close-Up View of a Flower (e.g., Pterocarpus indicus or Pterocarpus indicus) Pterocarpus indicus is the Narra Tree Note that for species name, genus and specific epithet should be separately underlined. Table 1. The Make Up of a Scientific Name Figure 2. Various Parts of a Leaf CLASSIFICATIONreview Arrangement of taxa into a particular order ○ Ranks levels of biological classification regardless of the criteria, groups are arranged according to hierarchical order. 1. Order (.e.g.Gentianales) - suffix: -ales 2. Family (e.g. Rubiaceae) - suffix: -oideae 3. Genus (e.g. Antherostele) 4. Species (e.g. Antherostele samarensis) REVIEW OF PLANT MORPHOLOGYreview Getting familiar with the terms used to describe plants is important in disting families, genera, and species of plants. ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK Figure 3. 8 Different types of Inflorescences 2 WHAT KINDS OF PLANT PHOTOS CAN WE TAKE? 6 ESSENTIAL ELEMENTS IN TAKING QUALITY PLANT PHOTOS SCIENCE AND ART Equipment ○ Visual, spatial, and temporal data Composition ○ Essential features (mainly taxonomic) Light and Color ○ Source, intensity, and effect Focus and Exposure ○ Magnification and resolution Accessories ○ Background, measurement, post-processing Considerations ○ Extraneous factors MACROPHOTOGRAPHY Macromorphology in life ○ taking photos of the whole structure of the plant in life while it is still alive. EQUIPMENT Camera ○ Digital single-lens reflex ○ Point-and-shoot ○ Cellphone Could take quality photos, provide GPS with specific apps Global positioning system receiver We not just want the visual data, but also the other data that comes with it or also called as metadata. It is also important to know the position where you collected the plant. Ex. If you get a plant in Luzon, it may produce a different compound when you get it from the members of the same species you will find on Mindanao. Date and time We are not just documenting morphological variations, we also want to document temporal variations in plants 🔊 Figure 5. Parts of a Flower specifically focusing on the androecium and gynoecium DOCUMENTATION OF LIFE What do we document in plants in life? o Preserve colors, three-dimensional structures, and habit o Show morphological, spatial, and temporal variations o Form a holistic mental image of a plant For many practical human activities, especially identification 🔊 🔊 🔊 🔊 Figure 4. Structure of a Flower’s Reproductive System WHY PHOTOGRAPH PLANTS? DEPENDS TO ITS SCALE Macrophotography ○ Documentation of gross structure, from habit shots to small features, usually in the field ○ Macromorphology Document overall structure of the plant from the field to small features Bigger picture, wholeness Photomicrography ○ Documentation of minutes features, from whole mounts to thin sections, usually in the lab ○ Histology, anatomy Usually we do this once we collect the plants, preserve them and collect in the lab ‌Mount the organs, very very thin section, or cross the plant organ to view the internal structure 🔊 🔊 🔊 🔊 support, Figure 6. Camera COMPOSITION 🔊 Documenting the natural appearance of the plant 🔊 features that need to be shown to identify the plant ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK 3 Standard: ○ Habit what it looks like in comparison to other plants ○ Vegetative System Stem close up and nodes most dichotomous keys rely on the difference in the feature (ex. leaf attachment) Leaf surfaces (ex. texture of the bark) ○ Reproductive system Inflorescence architecture Floral parts, fruit sections Cones, sori Reproductive systems should be documented in more detail. Special: ○ Specific diagnostic features Diagnose what group this plant is based on features that are specific to that family 🔊 🔊🔊 🔊 🔊 🔊 🔊🔊 🔊 Figure 8. Plant Photograph with Scale DIAGNOSTIC FEATURES OF A PLANT (IDEALLY THE) GENERAL FEATURES OF ANY PLANT Parts of a plant that are expected to be seen (and their ideal views in the photo): Figure 7. Ideal Views of A Plant Photograph ○ ○ ○ ○ ○ ○ ○ Details of the stem, be it a trunk or a twig Nodes - how the leaves are attached to the stem Leaves (although in the reference picture, there is no photo of the underside) If the leaves are compound, take note of the entire leaf because they have leaflets. Scars from snapped petioles are also important in identification. Inflorescence - a group of each flower Fruits (both young and mature) - to see ovules and how seeds are attached to the tissues of fruits (placentation) Flowers (both closed buds and open flowers) ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK Herbs may be tricky, so you have to take a really closer look. Scale is a significant component of a quality plant photo to describe how big a plant is. ○ The photo above is a flower of Vitex negundo (Lagundi). ○ Use rulers, tape measure, etc. ○ Sometimes, this can be edited during post-processing of the photo Figure 9. Non-Flowering Plant Photograph Figure 10. Male Cones (left) and Receptive Female Cones (right) Conifers (like Pine Trees) - non-flowering plants that bear seeds ○ Their seeds are tucked in cones ○ Cones may be males or females. Usually, male cones are smaller than females. ○ Seen in the photo above are male cones that release pollens. This makes people sneeze, especially those allergic to pollens. ○ Receptive Female Cones are open to receiving pollens at a particular stage. Once the ovules are fertilized by the sperm and pollen grain, the cone matures and becomes tough. 4 Figure 13. Bilateral Flower ○ Figure 11. Mature Cone ○ Stamens (male organs) should be noted (how close/far they are from each other). As the seeds mature, they become big and woody. Figure 12. Woody Cone Figure 14. Stamen Ferns - non-flowering plants that do not bear seeds at all (no flowers and fruits) but produce spores. ○ Spores are contained in Spori (singular: Sorus), usually black/brown spots or lining. ○ They are possessioned under the surface of a fertile/reproductive leaf ○ ○ Mints are usually documented only when they are ‘fruiting.’ Ovaries are usually four-lobed. TAXONS THAT HAVE SPECIFIC FEATURES EUDICOTS (MINT, BEAN, SUNFLOWER) ★ (1) Asterids-Lamiids Order: Lamiales Important identification: ○ Leaves opposite ○ Flower bilateral ○ A 2+2 ○ Gland-headed hairs ○ W/ 6-oxygenated ○ Flavones, oligosaccharide, verbascoside (acetoside) Figure 15. Four-Lobed Ovary cornoside, Family: Lamiaceae/Labiatae (Mint Family) Important identification: ○ Herbs or shrubs, aromatic with ethereal oils ○ Stem 4-sided ○ Leaves opposite ○ Inflorescence verticillaster or thyrse ○ Flowering bilabiate ○ G superior, deeply 4-lobed ○ Style gynobasic ○ Fruit schizocarp of nutlets ○ ○ ○ Mints have opposite leaves. The way they are attached to the stem exhibits ridges between the petioles. The flowers of mints are not necessarily radially symmetrical (like an ideal flower). In mints, they are Bilateral - and can be divided into two parts (left and right). The upper and lower lip of the flower may differ. ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK Examples: ○ Mentha x villosa Huds: (yerba buena) - lvs for cough, toothache, headache, dizziness, fainting, hysteria, gaseous distention, arthritis, and as mouthwash. ○ Ocimum basilicum L. (balanoy) - lvs for gaseous distention, functional dyspepsia ○ Ocimum tenuiflorum Burm. f. (sulasi) - lvs for tinea, ringworm, athlete’s foot ○ Coleus scutellarioides Elmer (mayana) - lvs for headaches and sprains ○ Premna adorata Blanco (alagaw) - lvs for headache ○ Vitex negundo L. (lagundi) - lvs for fever, headache, cough, and asthma. ★ (2) Rosids-Fabids Order: Fabales Important identification: ○ Symbiotic with root nodule bacteria ○ Flower papilionaceous (with wing, standard, keel) ○ A often 10 ○ G1 w/ numerous compartments ○ W/ Alkaloids, non-protein amino acids, lectins 5 Figure 19. Acacia Subfamily Flower Family: Fabaceae/Leguminosae (Bean Family) Important identification: ○ Leaves often compound, stipulate ○ Flowering 5-merous ○ G1 ○ Ovules numerous ○ Placentation marginal ○ Fruit legume ○ ○ ○ ○ Compound Leaves and how the Leaflets are arranged. A wide variety of the arrangement of petals is challenging to document. Most common sub-families are peanuts Placentation is also important in their plant photography. Examples: ○ Cassia fistula L. (kanya pistula) - constipation ○ Gliricidia sepium (Jacq.) Kunth ex Walp. (kakawati) - scabies and itching ○ Leucaena leucocephala (ipil-ipil) - intestinal worms ○ Senna alata (L.) Roxb. (akapulko) - scabies and tinea, ringworm and athlete’s foot ○ Senna occidentalis (L.) Link (balatong aso) tinea and athlete’s foot (Lam.) de Wit ★ (3) Asterids-Campanulids Order: Asterales Important identification: ○ Flower often bilateral ○ Pollination device (long style) ○ W/ inulin, sesquiterpenes, secoirioids Figure 16. Clitoria Ternatea ○ Sitaw, Bataw, and other vegetables would have tiny flowers that look like this: Family: Asteraceae/Compositae (Sunflower Family) Important identification: ○ Inflorescence head/capitulum ○ Subtended by involucre of phyllaries ○ Flower bilabiate, disk, or ray/ligulate ○ A syngenesious ○ G inferior ○ Ovule single, basal Figure 17. Bean Family Flower ○ ○ Alibangbang’s flowers are not as tiny as the peanut family’s but they have a different flower arrangement ○ ○ ○ Figure 18. Alibangbang Flower ○ Acacia’s subfamily does not necessarily have petals but they have numerous stamens. Take a closer photo of the stamens. ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK Composites have a peculiar flower because they are not just a single flower, but are composed of mini-flowers. Flowers in the middle are different from those in the periphery. Each one of the yellow flowers is a mini-flower called a floret. Get a longitudinal section to make sure you have details of the disc florets and ray florets. Best practice: Review first the diagnostic features of the specific candidate family your plant would most likely belong with. Example: ○ Chrysanthemum indicum L. (mansanilya) lvs for headache LIGHT AND COLOR Light source ○ Natural - ideal but depends on the time of the day. - generally, it is better to have more light, but not too much during the afternoon, - it is best to choose underexposure than overexposure (because it is harder to get data about your sample and you can post-process the photo) 6 ○ Flash White balance ○ Get as much detail as possible ○ If using sunlight as a light source, there may be shades that may alter the whiteness of your photo ○ Blue is the warmest color ○ If there’s a lot of shades/clouds, it may appear more ‘bluer’ or ‘purplish’ FOCUS AND EXPOSURE Subject vs. Background - It’s impossible to capture just the plant in its natural state. So make sure you focus on the subject, not the background. Working distance ↓, depth of field ↓, light requirement ↑ - The closer you get to the actual specimen, the shorter the working distance, the shorter the depth, and the HIGHER the light requirement. Movement of lens ○ Manual ○ Marco/supermacro mode Exposure - how much light you let illuminate your subject. ○ Aperture - opening size, e.g., f-stop; f/22 (↓) f/2.8 (↑) The higher the value of f-stop, the smaller aperture, the lesser the depth of field of the focus of your background. The lower the value of f-stop, the bigger the opening or aperture, and the depth of field increases, making the background blurry. ○ ISO - amount of light that reaches the sensor, 100-1600 In dim environments, you increase the ISO The more light you direct to the sensor of your camera, the more grainy the photo would be. ○ Shutter speed - opening time, e.g., 1/60s (↓) 1/1000s (↑) How much time you let the shutter open Slower shutter speed, would not detect movements Faster shutter speed will catch movements 🔊 🔊 🔊 🔊 🔊 🔊 🔊 Figure 21. Practical Application ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK ACCESSORIES Background ○ Best: Black (color) and felt (material) Scale ○ Black ruler (and a color palette if possible) Support ○ For camera: tripod ○ For subject: clay Editor ○ Background and stain remover CONSIDERATIONS Figure 20. Exposure Components In the photo above, the samples were taken with the same branch, same ISO (intensity of light) However Photo A has a bigger aperture, so the background is not visible. To capture the background more clearly, you have to decrease the aperture and reduce the shutter speed. Avoided: ○ Moisture ○ Wind Encouraged: ○ Studio PHOTOMICROGRAPHY Histology and anatomy in the lab ○ But specifically we do this for documenting plant tissues and plant cells in the laboratory. EQUIPMENT We deal with two-dimensional structure ○ So you make a cross section and then you mount it on a slide and you take a closer look at the microscope. Microscope ○ Stereo (1-10x) for more three-dimensional structures magnification is limited ○ Compound (100-1000x) closer look at thin sections of the plant organ Mounted camera (modern labs) ○ much easier to take photos (because it is connected to a software and saved automatically on computer) Link your specimen with the metadata, the original metadata, where it was found and when it was found. 🔊 🔊 🔊 7 ○ ○ if these are just tissues and you don't label them properly, unfortunately, you're gonna lose a lot of information, including the metadata. you may want to make sure that they are properly tagged and properly named in your files COMPOSITION We wanna see internal minute structures of the tissues in the cells. ○ The rule of thumb is to actually cover three tissues and three planes. ○ 3 tissues: Epidermal (outermost) Core tissue (vascular tissue, conducting tissue) Ground tissue (parenchyma, collenchyma, or sclerenchyma) Preparing Staining Sectioning ○ Whole mount ○ Cross/Transverse section ○ Longitudinal section Radial (median plane) Tangential (any plane closer to the surface of the plant organ, be it root or stem) ○ Macerated Mounting 🔊🔊 🔊 🔊 🔊 LIGHT AND COLOR Colors are given by stains ○ Staining is very important in plant micropitting as well. Light source and number Coarse and fine adjustment Stain FOCUS AND EXPOSURE They're no longer our problem. It's the problem of the microscope. Stereomicroscope (organs) - 1-10x Compound objectives (tissues, cells) ○ Scanner - 4x ○ Low power - 10x ○ High power - 40x ○ Oil immersion - 100x Electron microscope (ultrastructure) - 10,000,000x ACCESSORIES Background ○ Best: Black Scale ○ Ocular and slide micrometers Support ○ For camera: mount, software ○ For subject: clay, plate Editor ○ Background and stain remover SUMMARY OF MACROPHOTOGRAPHY AND PHOTOMICROGRAPHY Macrophotography Photomicrography Purpose Macromorphology Histology and anatomy Equipment Camera, GPS, Timestamp Camera, Microscope, Metadata Composition Diagnostic features Sections Light and Color Source, white balance Source, stain Focus and Exposure Lens work Objective work Accessories Background, scale, support, editor Background, scale, support, editor Considerations Control of moisture, wind Cost, byproducts Table 2. Macrophotography vs Photomicrography OPEN-FORUM PORTION CONSIDERATIONS Cost Byproducts ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK Macrophotography and Photomicrography are two important photography skills that we want to know on the scale of documentation of plants. For macrophotography, the rule of thumb is to take photos of plants the way you would describe them, and you would want to describe them as accurately as possible because you would want to accurately identify them with your eye. ○ For photomicrography, fortunately, microscopes do it for us, but for macro photography, you do it on your own. Accessories are typically the same, but considerations depending on the for macrophotography, usually it's the outside environment, environmental conditions that you need to consider. ○ For photomicrography, usually it's the lab conditions that you want to consider. How much editing is allowed in plant photography? ○ Rule of thumb is as long as it still stays as natural as it could be. ○ If you want to remove something, you may want to just be explicit about that in the caption, like in the title of your figure. ○ It is also a matter of honesty. Would it be okay for us to consult Digital Flora or its Facebook page? Can we send pictures there so the botanist can help identify our plant samples? 8 ○ Students, as well as faculty, really, are encouraged to seek help from botanical experts. ○ The rule of thumb is to let the identifier do their job, first and foremost. And your job is to have a candidate identity or identification for your plant. ○ We don't necessarily let other people, especially botanists, identify on our behalf. We just let them verify our plant identifications. botanists are really discouraging us that we can identify it right away. We don't want other people to identify it, we identify it first, then we seek help from others to verify our identity. ○ When you post on COS Digital Flora of the Philippines, you need to have an initial identification already so that the botanists in COS Digital Flora of the Philippines can verify. And they are very helpful. If they know that you got it wrong, they will lead you to more sources for you to be able to identify it. Some of the institutions that would release a certificate of authentication for their plant would be online now. So, instead of bringing to them actual samples of their plant, they would require either photographs of their plant or, as the student mentioned here, pictures of their herbarium specimen. So, between photographs of the plant or photographs of the herbarium specimen, which is much better for this process? ○ Both. Like, the best files to submit to the National Herbarium, for example, to any herbarium for authentication or to any botanical expert for authentication would be both the photos in their natural state and the photos of the herbarium specimen. How can we best reflect the height or size of a whole plant, especially a tree, when we are taking the photo in its habitat? ○ It will really take frequent fieldwork to be used to measuring by eye. ○ There's no proper technique because it's really hard, especially if we have different experiences with plants. Just describe it as articulately as possible. How can you ensure though that the pictures are actually attributable to the one who took the picture and then piracy would be avoided? ○ Intellectual property. As far as botanical photographers are concerned, as far as plant photographers are concerned, as long as you get permission, first and foremost. As long as you're following the fair use policy, for academic purposes, for educational purposes, botanical photographers won't mind sharing them. But at least cite them. Like copyright. 🔊 🔊 🔊 🔊 ARCANGEL, DOCUYANAN, MALONZO, MATAAC, PARK 9