Common Terms

Common Terms

Arthropod – an invertebrate with jointed legs. They are divided into four major groups: insects; myriapods (including centipedes and millipedes); arachnids (including spiders, mites, ticks, and scorpions); and, crustaceans (including slaters, prawns, and crabs).

Assay – experimental methods for assessing the presence, localization, or biological activity of a substance in living cells and biological matrices.

Beta-testing – beta testing is an opportunity for users to use a product and/or technology (e.g., SOPs, mobile application) in a production environment (i.e., field or laboratory) to uncover any issues or challenges before general release.

Bioinformatics – bioinformatics, as related to genetics and genomics, is a scientific subdiscipline that involves using computer technology to collect, store, analyze, and disseminate biological data and information, such as DNA and amino acid sequences or annotations about those sequences. Scientists and clinicians use databases that organize and index such biological information to increase our understanding of health and disease and, in certain cases, as part of medical care.

Biosurveillance – systematic data-gathering to survey the environment or a location of interest for viruses, bacteria, fungi and/or other biological entities that might cause disease and pose a threats to human, animal or plant health to achieve early warning of health threats, early detection of health events, and overall situational awareness of disease activity.

BLAST – (Basic Local Alignment Search Tool) is a software tool for searching similarity in nucleotide sequences (DNA) and/or amino acid (protein) sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

CZID – Chan Zuckerberg ID is an open-source metagenomics analysis for researchers to rapidly identify new and emerging infectious diseases.

Deoxyribonucleic Acid – (abbreviated DNA) is the molecule that carries genetic information for the development and functioning of an organism. DNA is made of two linked strands that wind around each other to form a double helix.

Ectoparasite – an ectoparasite is a parasite that lives externally on another animal but does not kill it, such as ticks and fleas.

e-MERGE System – an electronic platform and centralized data repository for all human, animal, and environmental surveillance data collected by DoD and global partners to detect, monitor, and mitigate emergent environmental pathogens.

Eschar – dead tissue that forms over healthy skin and then, over time, falls off.

Eukaryotic – (of a cell) a cell that contains membrane-bound structures. It is the basis for every multicellular organism, including animals, plants, humans, and some unicellular organisms, such as protozoa.

External Opportunistic Sample – iDNA, eDNA, and/or vDNA samples obtained through established Material Transfer Agreements (MTA) with non-REDI-NET Consortium partners and based on locally approved protocols, including the assistance of local veterinarians and trained personnel for sample collections. See the Opportunistic Samples page for details on this process.

Flinders Technology Associates (FTA) Cards® – a chemically treated filter paper designed to collect, preserve, and ship biological samples for subsequent DNA and RNA analysis. Special chemicals on the filter paper lyse and inactivate bacteria and viruses and preserve their DNA and RNA for detection by PCR.

Hematophagous – (of an animal/insect) feeding on blood. Blood-feeding insects are important vectors that can transmit an array of zoonotic pathogens.

Homogenized – (of the water column during sampling) mixed so that all the parts of the water column are the same.

Internal Opportunistic Sample – invertebrate samples (e.g., tick and/or leech) collected off the body and/or clothing of field personnel while conducting field sampling or vertebrate samples (e.g., feces) collected in passing while doing field sample collections.

Ligation-Based Library Preparation – ligation-based library preparation is a process where adapters, or small known synthetic DNA sequences, are ligated to DNA fragments. There are three primary steps to ligation-based library prep: fragmentation, ligation of adapters, and PCR (optional).

MEGAN – (MEtaGenome Analyzer) is a computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.

Metadata – represents data about data. Metadata enriches the data with information, which makes it easier to discover, use, and manage.

MiniMap – is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database.

Metagenomics – the study of the structure and function of entire nucleotide sequences isolated and analyzed from all the organisms (typically microbes) in a bulk sample. Metagenomics is often used to study a specific community of microorganisms, such as those residing on human skin, in the soil, or in a water sample.

Negative Control – is characterized by the absence of reagents or components necessary for successful analyte detection. By not exposing the negative control group to the experimental treatment (or any other treatment), they are not expected to produce any result due to any variable in the experiment and may serve as the “baseline.”

Next-Generation Sequencing – (abbreviated NGS) is a massively parallel sequencing technology that offers ultra-high throughput, scalability, and speed. The technology is used to determine the order of nucleotides in entire genomes or targeted regions of DNA RNA.

Nucleic Acid – large biomolecules (e.g., DNA and RNA) that play essential roles in all cells and viruses. A major function of nucleic acids involves storing and expressing genomic information.

One Health – One Health is a collaborative, multisectoral, and transdisciplinary approach — working at the local, regional, national, and global levels — with the goal of achieving optimal health outcomes, recognizing the interconnection between people, animals, plants, and their shared environment.

Pathogen – an organism (e.g., virus, bacteria, fungi, parasite) that causes disease to its host.

Polymerase Chain Reaction – (abbreviated PCR) is a laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA, which can then be studied in greater detail. PCR involves using short synthetic DNA fragments called primers to select a segment of the genome to be amplified and then multiple rounds of DNA synthesis to amplify that segment.

Positive Control – is used to assess the test validity of the experimental protocol or equipment by producing the expected result.

Quantitative Polymerase Chain Reaction – (abbreviated qPCR) adds two elements to the standard PCR process: fluorescent dye and a fluorometer. qPCR uses similar DNA amplification conditions as in conventional PCR but can detect the PCR product in real-time without needing agarose gel electrophoresis and quantifying the sample’s amount of template DNA.

Ribonucleic Acid – (abbreviated RNA) is a nucleic acid present in all living cells, structurally similar to DNA, but with only a single, helical strand of bases.

Risk Estimation – (also referred to as risk characterization) is the final step in risk assessment to produce measures of the health, safety, and environmental risks being assessed.

Risk Model – a risk model is a mathematical representation of a system, commonly incorporating probability distributions and using relevant historical data, scientific evidence, and expert opinion to understand the probability of a risk event occurring and its potential severity.

Sequencing – a process used to determine the order of nucleotides (e.g., in DNA and RNA) in small targeted genomic regions or entire genomes.

Surveillance – in public health, surveillance is the ongoing systematic collection, analysis, and interpretation of data, closely integrated with the timely dissemination of these data to those responsible for preventing and controlling disease and injury.

Vector – living organisms (e.g., mosquitoes, ticks, triatomes) that can transmit infectious pathogens between humans, or from animals to humans.

Vector-Borne Disease(s) – (abbreviated VBD) are human illnesses caused by parasites, viruses, and bacteria that are transmitted by vectors.

Xenosurveillance – is a technique that uses blood collected by hematophagous arthropods (e.g., mosquitoes, leeches, ticks) to monitor and identify vertebrate pathogens.

Zoonotic – (of a disease) able to spread from animals to humans. Zoonotic diseases (also known as zoonoses) are caused by pathogens, such as viruses, bacteria, parasites, and fungi, that spread between animals and people.