Biotechnology Terms Starting With N
Biotechnology Glossary: N
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Nanobody
/ NAN-oh-bod-ee / · From Greek nanos, dwarf, plus body, referring to small antibody fragment
Nanobody is a small antigen-binding protein consisting of a single variable domain derived from the heavy-chain-only antibodies of camelids, typically 12 to 15 kilodaltons in molecular weight.
Nanobodies measure approximately 2.5 nanometers in diameter, roughly four times smaller than a conventional IgG antibody, and maintain high binding affinity through elongated CDR3 loops that can reach into enzyme active sites and receptor cavities inaccessible to larger molecules. Hamers-Casterman and colleagues discovered heavy-chain-only antibodies in dromedary camels (Camelus dromedarius) in 1993, and the single variable domains were subsequently named nanobodies by the Belgian company Ablynx. Production in Escherichia coli or yeast costs roughly 90 percent less than mammalian cell-based antibody manufacturing and can yield up to 10 grams of purified protein per liter of culture.
Caplacizumab, approved in 2018 for thrombotic thrombocytopenic purpura, became the first nanobody therapeutic on the market, with more than 20 additional nanobody candidates now in clinical trials for cancer, inflammation, and infectious diseases. Their compact structure also confers exceptional stability, allowing storage at room temperature for months and resistance to pH extremes that would denature conventional antibodies.
Nurse sharks (Ginglymostoma cirratum) independently evolved a form of single-domain antibody called a VNAR, structurally analogous to camelid nanobodies, suggesting that compact single-domain antigen binding arose at least twice in vertebrate evolution separated by roughly 450 million years.
Nanobodies are entirely synthetic creations with no natural counterpart. Nanobodies are derived from heavy-chain-only antibodies that occur naturally in the blood of camelids, including llamas, alpacas, dromedary camels, and Bactrian camels, where they constitute roughly half of the circulating antibody repertoire.
Researchers at the Vlaams Instituut voor Biotechnologie immunized alpacas (Vicugna pacos) with HIV envelope proteins and isolated nanobodies capable of neutralizing 96 percent of tested HIV strains at concentrations below 1 nanomolar, a breadth of neutralization far exceeding that of most conventional monoclonal antibodies tested against the same panel. The selected nanobodies targeted the CD4 binding site on gp120, a conserved epitope largely inaccessible to conventional antibodies due to steric constraints, but reachable by the nanobody's protruding CDR3 loop of approximately 17 amino acids. Bacterial production of the lead nanobody at milligram scale required only 48-hour fermentation in E. coli, yielding active protein at purities above 95 percent without affinity chromatography.
Nanopore Sequencing
/ NAN-oh-por SEE-kwen-sing / · From Greek nanos, dwarf, plus pore from Latin porus, plus sequencing
Nanopore sequencing is a DNA and RNA sequencing method that identifies nucleotides in real time by measuring characteristic changes in electrical current as a single-stranded molecule passes through a protein nanopore embedded in a membrane.
Oxford Nanopore Technologies commercialized the approach using biological pores derived from bacterial membrane proteins, applying a voltage that drives a DNA strand through the 1.2-nanometer channel at approximately 450 bases per second while current is sampled at 4,000 measurements per second. Each nucleotide produces a characteristic disruption in ion flow, and machine-learning algorithms convert the current trace into a base sequence in real time. Read lengths routinely exceed 100,000 bases and can surpass 2 million bases, more than 100 times the typical output of Illumina short-read sequencing, enabling assembly of complete chromosomes from telomere to telomere.
Raw per-read accuracy of approximately 95 percent improves to 99.9 percent through consensus calling across multiple overlapping reads. The portable MinION sequencer weighs just 100 grams and connects to a laptop via USB, a form factor that supported rapid pathogen sequencing during the 2014 to 2016 Ebola outbreak in Guinea.
Nanopore sequencing detects DNA methylation and other base modifications directly from the electrical signal without any chemical conversion step, providing epigenetic information that bisulfite sequencing and most short-read platforms cannot capture in a single experiment.
Nanopore sequencing is less accurate than Illumina sequencing and therefore inferior for all applications. Ultra-long nanopore reads resolve structural variants and span entire repetitive genomic regions that short-read assemblies cannot reconstruct, making the two platforms complementary rather than interchangeable.
Scientists at UC Santa Cruz and the Telomere-to-Telomere consortium used nanopore sequencing to complete the first gapless human genome assembly, published in 2022; reads averaging 50,000 bases spanned centromeric arrays containing millions of tandem repeats, filling the roughly 8 percent of the genome that had remained unsequenced since the original Human Genome Project. The consortium sequenced the CHM13 cell line to approximately 60-fold coverage, generating over 100 gigabases of ultra-long reads using Oxford Nanopore PromethION flow cells running R9.4.1 pores at 400 millivolts. Assembly required specialized algorithms capable of resolving the extreme repeat content of pericentromeric regions, where individual repeat units measuring 171 base pairs appear in tandem arrays spanning up to 5 megabases.
Next Generation Sequencing
/ NEKST jen-er-AY-shun SEE-kwen-sing / · Old English niehst; Latin generatio; Latin sequi
Next generation sequencing is a set of massively parallel DNA sequencing technologies that simultaneously sequence millions of DNA fragments, enabling rapid, cost-effective analysis at the scale of whole genomes, transcriptomes, or microbiomes.
NGS transformed biology by reducing the cost of sequencing a human genome from roughly 3 billion dollars, the price of the original Human Genome Project completed in 2003, to under 1,000 dollars by 2014. Illumina short-read platforms dominate clinical and research markets, generating hundreds of gigabases of data per run with per-base error rates below 0.1 percent, while PacBio and Oxford Nanopore instruments produce longer reads suited to structural variant detection and de novo genome assembly. Sample preparation involves fragmenting DNA, ligating adapter sequences, amplifying the library, and loading it onto a flow cell where millions of fragments are sequenced in parallel.
Applications span whole-genome sequencing, RNA sequencing, ChIP-seq for chromatin immunoprecipitation, metagenomic profiling of microbial communities, and somatic mutation detection in tumor biopsies. During the COVID-19 pandemic, NGS platforms sequenced more than 16 million SARS-CoV-2 genomes deposited in the GISAID database, enabling real-time global surveillance of emerging variants.
The first NGS platform to reach commercial scale, the 454 pyrosequencing system launched by 454 Life Sciences in 2005, could sequence an entire bacterial genome in a single four-hour run, a task that had previously required weeks of Sanger sequencing across dozens of capillary instruments.
NGS produces one long, continuous chromosome sequence directly from the instrument. NGS instruments generate millions of short sequence reads that bioinformatics software must align to a reference genome or assemble de novo before any chromosome-level sequence can be interpreted.
Public health laboratories used Illumina NGS to sequence the genomes of Listeria monocytogenes isolates during a 2011 cantaloupe outbreak in the United States; whole-genome comparisons across 147 patient isolates identified a single farm as the source within days, a resolution impossible with the pulsed-field gel electrophoresis typing methods previously used for outbreak investigation. Each genome was sequenced to approximately 40-fold coverage using 100-base paired-end reads, with assembly producing contigs covering 98 percent of the 3-megabase reference genome. Core-genome single nucleotide variant analysis distinguished isolates differing by as few as two SNVs, sufficient to separate the outbreak cluster from background environmental strains collected from the same county.
Nuclear Reprogramming
/ NOO-klee-ur REE-proh-gram-ing / · From Latin nucleus, small nut or kernel, and programma, from Greek programma, public notice or written instruction.
Nuclear Reprogramming is the process of converting a differentiated cell back to a pluripotent or totipotent state by altering its gene expression patterns.
Nuclear reprogramming reverses cellular specialization by resetting the epigenetic marks that define cell identity. Shinya Yamanaka pioneered this field in 2006 by demonstrating that just four transcription factors, Oct4, Sox2, Klf4, and c-Myc, could reprogram adult mouse fibroblasts into induced pluripotent stem cells. This breakthrough earned him the Nobel Prize in 2012 and revolutionized regenerative medicine by providing an alternative to embryonic stem cells.
The efficiency of reprogramming typically ranges from 0.01% to 1%, and the process takes 2 to 4 weeks under optimal conditions. Modern approaches now include chemical reprogramming using small molecules and direct lineage conversion without passing through a pluripotent intermediate state.
Nuclear reprogramming can turn skin cells into neurons without ever becoming stem cells first, a process called transdifferentiation that bypasses the pluripotent stage entirely. Scientists have even reprogrammed human cells into mouse-like cells by changing just the species-specific transcription factor expression patterns.
Nuclear reprogramming erases all cellular memory completely. Reprogrammed cells often retain epigenetic traces of their tissue of origin, a phenomenon called epigenetic memory that can bias their differentiation potential and must be screened for in therapeutic applications.
In laboratory settings, researchers routinely reprogram human dermal fibroblasts obtained from skin biopsies into induced pluripotent stem cells that can then differentiate into cardiomyocytes for heart disease research. The Gladstone Institutes in San Francisco maintain extensive iPSC banks derived from patients with genetic diseases through nuclear reprogramming.