moving the lamppost

random musings of a molecular biologist turned code jockey in the era of big data and open science.


dengue fever
a tropical disease caused by one of four species of dengue viruses characterized by fever, headache, muscle and joint pains, and a skin rash similar to measles.
a document submitted in support of candidature for an academic doctorate qualification presenting the candidate’s research and findings.
effector gene
in this sense: a gene that will cause the desired change in the environment of the mosquito or other vector. An example might be a gene that codes for a protein that targets and destroys the pathogen.
an organism whose cells contain complex structures (particularly a nucleus containing the genome) enclosed within membranes. Other membrane-bound structures exist as well.
not originating from the system to which the object is being applied.
gene drive
molecular genetic tactics that cause a linked trait or gene to spread through a population at faster rates than expected based on fitness alone; generally operating independently of natural selection and genetic drift.
the sum of an organism’s genetic material (RNA or DNA).
the specific genetic sequence of an individual organism. example: the mutation in an eye color gene that results in blue eyes.
the insect analog of a circulatory system.
a measure of the frequency with which new cases of illness, injury, or other health condition occurs among a population during a specified period.
a tropical disease caused by one of multiple species of protist in the genus Plasmodium characterized by recurring cycles of fever and headache.
the location in the mosquito’s digestive system where the bloodmeal is processed.
any observable genetic trait of an individual organism. examples: eye color, height, malformed wings, feathers, scales, venom, etc
the number or proportion of cases or events or attributes among a given population.
In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA.
reporter gene
In molecular biology, a reporter gene (often simply reporter) is a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals or plants. Certain genes are chosen as reporters because the characteristics they confer on organisms expressing them are easily identified and measured (cause the cells to glow), or because they are selectable markers (allow only the cells with the reporter to survive in the presence of a poison).
RNA-seq, also called “Whole Transcriptome Shotgun Sequencing” (“WTSS”), refers to the use of high-throughput sequencing technologies to sequence cDNA in order to get information about a sample’s RNA content. The technique has been adopted in studies of diseases like cancer. With deep coverage and base-level resolution, next-generation sequencing provides information on differential expression of genes, including gene alleles and differently spliced transcripts; non-coding RNAs; post-transcriptional mutations or editing; and gene fusions.
Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme, RNA polymerase.
transcription factor
In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes.
a (usually functional) gene that has been transferred from one organism to another.
a process by which exogenous DNA sequences (sometimes termed transgenes) are introduced to a host organism (usually with the goal of performing a novel function in the host).
Translation is the process by which amino acids are polymerized into proteins by reading the information encoded on strands of mRNA.
transmission cycle
the cycle by which a pathogen is transmitted from one host to another.
transposable element
relatively short regions of DNA in an organism’s genome that have the ability to cut (or copy) themselves from the genome and insert themselves into a new location in the genome. (More information on different types and behaviors of TEs)
an organism that facilitates the transfer of pathogens from one host to another.