collections and databases

Natural History Collections

repositories of specimens representing the natural world; specimens are preserved and organized for scientific study, education, and public display

What is the importance of the Natural History Collections?

They provide a tangible record of Earth’s history and evolution; it documents the diversity of life and enables us to identify biodiversity hotspots

Enumerate the types of biological collections

1. Botanical

2. Zoological

3. Microbial and Tissue Fungarium

4. Fungarium / Fungal Collection

5. Geological Collections

6. Molecular and Genomic Collections

Herbarium

A collection of preserved plant specimens; plants are dried, pressed, and mounted

Enumerate the types of zoological collections

1. Mammal Collections

2. Bird Collections / Ornithological

3. Reptile and Amphibian Collections / Herpetological

4. Fish Collections / Ichthyological

5. Insect Collections / Entomological

6. Marine Invertebrate Collections

Microbial / Tissue Collections

Collections of microorganisms and macroorganisms (tissue) for their genetic material to support research in evolution, taxonomy, and biotechnology

Enumerate the type of microbial / tissue collections

1. Type strains

2. Cryopreserved specimens

3. Lyophilization

4. Tissue repositories

Lyophilization

freeze-drying process turns microbial cultures into stable powders, allowing for safe, long-term storage and easy international shipping

Tissue repositories

collections of specific biological samples (like muscle or blood) primarily for DNA and RNA sequencing to study evolutionary relationships.

Type strain

are the definitive living benchmarks for microbial species; they serve as the "original reference" used to identify and name new organisms

Cryopreserved specimens

are stored in cryovials at ultra-low temperatures (-80°C to -196°C) to halt biological aging and prevent genetic drift over decades

Fungarium / Fungal Collections

repositories dedicated to the preservation of fungal specimens for taxonomic & evolutionary research

Enumerate the types of fungarium / fungal collections

1. Cryopreserved

2. Micro-morphological slides

3. Modern fungaria

4. Metadata and Field notes

Metadata and Field notes

information that provides a historical record of the fungal diversity; it records notes for every specimen and its host, substrate, and ecological habitat

Modern fungaria

they store small tissue samples in silica gel or ultra-low freezers to preserve high-quality genomic DNA for molecular phylogenetics and barcoding

Micro-morphological slides

permanent microscope slides of gills, pores, or specialized cells, as these tiny structures are critical for distinguishing between nearly identical species

Cryopreserved

living fungi are preserved in liquid nitrogen or on agar slants to study growth patterns and biochemical properties

Enumerate the types of geological collections

1. Mineralogical Collections

2. Petrological Collections

3. Paleontological Collections

Mineralogical Collections

Contain specimens of minerals, which are naturally occurring solid substances with a specific chemical composition and crystal structure. Minerals are categorized by their Properties. Used to study mineralogy, geology, and materials science

Petrological Collections

Contain samples of rocks, which are composed of one or more Minerals. Rocks are classified by how they formed (igneous, sedimentary, metamorphic). Used to study the Earth's history, geological processes, and the formation of landscapes

Paleontological Collections

Fossil Collections; they contain preserved remains or traces of ancient organisms. Fossils provide evidence of past life and help us understand evolution and the history of the Earth

Enumerate the types of molecular and genomic collections

1. National Library of Medicine (GenBank)

2. BoldSystems

3. EMBL-EBI

UP Arboretum

This is the last urban rainforest in metro manila

eDNA

Environmental DNA; genetic materials that organisms naturally shed into their surroundings (environment)

Digitization

converting specimens and data to digital formats; it promotes accessibility, preservation and accelerated research

Database Development

Improving databases for managing and linking data

FAIR principles

Findable: can be easily located

Accessible: data is available and can be retrieved

Interoperable: can be integrated and it matches with other datasets

Reusable: the data can be used for future research

Modernization

1. Genomics & bioinformatics

2. 3D imaging

3. Stable isotope analysis

4. eDNA

Genomics & bioinformatics

analysis of the organism’s entire DNA code to figure out what species it is, its evolutionary relatives, and how it functions

3D imaging

enables us to generate a perfect, 3D virtual models of specimens

Stable isotope analysis

it analyses the tissues of an organism to figure out what it eats, its position in the food chain, and what parts of the world it migrated through