Alveoli are tiny sacs within lungs that allow oxygen and carbon dioxide to move between the lungs and bloodstream.
The study of the structures of organisms.
- Anatomical Structures
The bodily structure of a plant or an animal or of any of its parts.
- Anatomy Tree
Anatomical structures from the developing mouse and human lower respiratory tract system and their relationships are displayed as a tree.
A note of explanation or comment added to text or diagram.
An antigen is any substance that causes the immune system to produce antibodies against it. An antigen may be a foreign substance from the environment, such as chemicals, bacteria, viruses, or pollen. An antigen may also be formed inside the body, as with bacterial toxins or tissue cells.
- Assay Type
Analysis done to determine the presence of a substance and the amount of that substance.
Bioinformatics REsource ATlas for the Healthy lung is a highly functional, publically accessible platform which facilitates analysis of data generated by LungMAP Research Centers.
A bronchus (plural Bronchi) is a passageway in the respiratory tract that conducts air into the lungs. There is a right bronchus and a left bronchus and these bronchi branch into smaller secondary and tertiary bronchi which branch into smaller tubes, known as bronchioles.
The bronchioles or bronchioli are the passageways by which air passes through the bronchi to the alveoli (air sacs) of the lungs. They are branches of the bronchi, and are part of the conducting zone of the respiratory system.
Firm, whitish, flexible connective tissue found in various forms in the larynx and respiratory tract, in structures such as the external ear, and in the articulating surfaces of joints.
The smallest structural and functional unit of an organism, typically microscopic and consisting of cytoplasm and a nucleus enclosed in a membrane.
It is the space between the nucleus and the outer cell membrane, which is composed of the cytosol, i.e., a fluid containing water-soluble molecules, and organelles with specific cell functions, such as the mitochondria and endoplasmic reticulum.
Away from the attachment, origin, or point of reference of the organ or structure.
- Eukaryotic Cells
Cells which contain a nucleus and are mainly found in multi-cellular organisms. They also contain organelles which serve a specific job in the cell.
A gene is a small piece of genetic material, or coded DNA segment that contains within it a set of instructions for making molecules that organisms need to function properly.
- Gene Expression
Genes cannot be used directly by an organism. Instead they must be turned into a gene product, i.e., RNA and/or protein. Gene expression is the process by which the information contained within a gene becomes a useful product.
- Hierarchical Clustering
Hierarchical clustering involves creating clusters that have a predetermined ordering from top to bottom.
Part of an organ where structures such as blood vessels and nerves enter.
- Hyaline Cartilage
Translucent bluish-white type of cartilage present in the joints, the respiratory tract, and the immature skeleton.
Immunofluorescence is a powerful technique that utilizes fluorescent-labeled antibodies to detect specific target antigens.
In situ hybridization (ISH) is a molecular technique used to detect local patterns of gene expression within cells and tissues by assaying the net amounts of mRNA encoded by a specific gene at a given time.
The hollow muscular organ forming an air passage to the lungs and holding the vocal cords in humans and other mammals.
Lipidomics is the study of the structure and function of the complete set of lipids (the lipidome) produced in a given cell or organism as well as their interactions with other lipids, proteins and metabolites.
Fluid containing infection-fighting white blood cells, found throughout the body.
- Lymphatic System
Network of tissues and organs that help rid the body of toxins, waste and other unwanted materials. The primary function of the lymphatic system is to transport lymph.
- Lymphatic Vessel
Lymphatic vessels are structures of the lymphatic system that transport fluid away from tissues. Lymphatic vessels are similar to blood vessels, but they do not carry blood. The fluid transported by lymphatic vessels is called lymph.
- Mass Spectrometry
Mass spectrometry (MS) is an instrumental method for identifying the chemical constitution of a substance by means of the separation of gaseous ions according to their differing mass and charge.
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) or DNA immunoprecipitation sequencing (DIP-Seq) is commonly used to study 5mC or 5hmC modification. Specific antibodies can be used to study cytosine modifications.
- Molecular Pathway
A series of actions among molecules in a cell that leads to a certain end point or cell function.
Messenger RNA (mRNA) is a subtype of RNA. An mRNA molecule carries a portion of the DNA code to other parts of the cell for processing. mRNA is created during transcription. During the transcription process, a single strand of DNA is decoded by RNA polymerase, and mRNA is synthesized
miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3'-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing
- nano-string assay
Uses the nCounter Analysis System, digital technology that enables direct multiplexed measurement of gene expression and offers high levels of sensitivity and precision, including detection of fractional fold change differences. The technology uses molecular barcodes and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.
Nanospray desorption electrospray ionization (Nano-DESI) is an ambient method for liquid-extraction surface sampling in mass spectrometry.
A bundle of fibers that uses electrical and chemical signals to transmit sensory and motor information from one body part to another.
Spherical mass of protoplasm encased in double membrane and found in most eukaryotic cells, directing their growth, metabolism, and reproduction, and functioning in the transmission of genic characters. It is the location of the cell's DNA.
“Omics” refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism. Examples include genomics, proteomics, and lipidomics.
An ontology is a description of what exists. It includes entities (things or processes) and their relationships. An anatomy ontology comprises anatomical structures (e.g. lung) and their structural (part-of) and type (is-a) relationships. Some anatomy ontologies, including the LungMAP ontology, also include temporal relationships (exists at stages X to Y). The anatomy ontology facilitates annotation of gene expression patterns by providing standard names for structures. It also facilitates data mining by providing descriptions of the relationships between structures. The LungMAP ontology is a hierarchy of histologically defined anatomical structures for canalicular to alveolar stages in the developing mouse and postnatal human lower respiratory tract system.
Organized structure in a cell that performs a specific function.
An individual living thing that can react to stimuli, reproduce, grow, and maintain homeostasis. It can be a virus, bacterium, protist, fungus, plant or animal.
A sequence of chemical reactions undergone by a compound or class of compounds in a living organism.
Two types of probes are used to generate data for LungMAP: 1) a DNA or RNA hybridization probe used to detect the presence of its complementary nucleotide sequence by binding to that site; and 2) an antibody probe used to detect a specific target protein by binding to its antigenic sites. Subsequent detection or visualization of labeled DNA/RNA and/or antibody binding to their gene products is used to assay gene expression in the tissue, cell, or structure of interest.
“Proteome” refers to the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or a cellular system.
Proteomics is a large-scale comprehensive study of a specific proteome, including information on protein abundances, their variations and modifications, along with their interacting partners and networks, in order to understand cellular processes.
The ground substance of living material and, hence, responsible for all living processes. It contains two major divisions: cytoplasm and nucleoplasm (cell nucleus).
Closest to the attachment, origin, or point of reference of the organ or structure.
Thin serous membranes enveloping the lungs (visceral pleura) and lining the inner walls of the thoracic cavity (parietal pleura). A thin film of fluid (pleural fluid), secreted into the space (pleural cavity) between these two linings, acts as a lubricant, allowing the membranes to glide smoothly during respiration.
- Pulmonary Artery
Artery that carries blood from the right ventricle of the heart to the lungs.
- Pulmonary Capillary Bed
Capillaries that are in the lung.
Ribosomes are organelles where proteins are made.
Ribonucleic acid (RNA) is a transcript of the genetic code found within the nucleus of the cell.
RNA-seq is a method to quantify, discover and profile RNAs. It produces millions of sequences from complex RNA samples.
The tube in humans and other air-breathing vertebrates extending from the larynx to the bronchi, serving as the principal passage for conveying air to and from the lungs; the windpipe.
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes falsely called primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule.
- Signature Gene List
A group of genes (aka signature) whose combined expression pattern is uniquely characteristic of a biological/cellular/molecular phenotype. Through various novel bioinformatics analyses, LungMAP researchers have generated signature genes in developing lung tissues, some of which are novel observations that may challenge existing knowledge. The gene lists comprise knowledge that is both temporal and dynamic as the research continually evolves.
The collective descendants of a common ancestor; a race, stock, line, or breed.
- Standard Deviation
Measure that is used to quantify the amount of variation or dispersion of a set of data values. A standard deviation close to zero indicates that the data points tend to be very close to the mean.
- Time Course Experiment
Time-course experiments require that the levels of different data like proteins and lipids are observed in a cell at different time points over the course of a given time frame.
A group or layer of similarly specialized cells that together perform certain specific functions.
- Type I Pneumocyte
The cell responsible for the gas (oxygen and carbon dioxide) exchange that takes place in the alveoli.
- Type II Pneumocyte
The cell responsible for the production and secretion of surfactant, the molecule that reduces the surface tension of pulmonary fluids and contributes to the elastic properties of the lungs.
Vibratome assisted subsurface imaging microscopy (Vibra-SSIM) is an imaging method in which a vibrating tissue sectioning system is coupled to a microscope. The sectioning of the sample occurs under a surface of an aqueous buffer in a basin. A positioning system enables the microscope to image adjacent sub-regions of the sample.
- Visualization Method
Any one of a variety of detection systems, such as an enzymatic reaction or fluorescent label, used to visualize and then record nucleotide or antibody binding to target gene products in tissues or cells.
A Z-Score is a statistical measurement of a score's relationship to the mean in a group of scores. A Z-score of 0 means the score is the same as the mean. A Z-score can also be positive or negative, indicating whether it is above or below the mean and by how many standard deviations.