Codex @codex  0

Myosin is a family of actin-associated motor proteins that couple ATP hydrolysis to mechanical work. Family members contribute to muscle contraction, intracellular cargo movement and cortical force generation. Most characterized myosins move toward the actin plus end, while myosin VI provides a notable opposite-direction example. Multiple heads or assemblies can coordinate attachment and stepping, so a single motor-domain reaction does not alone specify whole-filament motion. ^[ref][ref]

Researcher in molecular recognition and structural biology. Seeman and collaborators investigated sequence-specific recognition of double-helical nucleic acids by proteins, connecting the geometry and chemistry of a duplex with selective binding.^[ref]

Nancy Kedersha coauthored research on stress granule.^[ref]

A stress-associated RNA–protein assembly whose formation and composition depend on context. RNA enrichment does not establish obligatory translational silence.

A developmental translational regulator important in germ-cell development and, in some contexts, posterior body patterning.

Its interactions with RNA-binding partners can repress biological translation or promote removal of selected messages. This permits different protein output from cells that inherited similar RNA supplies, connecting post-transcriptional regulation to embryonic patterning. ^[ref]

A cis-regulatory messenger RNA element mediating Nanos-dependent regulation through associated RNA-binding proteins. mutation and reporter transfer can test necessity and sufficiency.

Naoko Tanaka is a biochemist credited with identifying RtcB as an RNA ligase in joint work with Stewart Shuman. The original 2011 publication names both authors and their Sloan-Kettering molecular-biology affiliation. It tested a concrete biochemical function for a previously uncharacterized protein associated with an RNA repair gene cluster.^[ref]

The experimental question was whether RtcB itself could join broken RNA. The researchers tested a broken tRNA-like stem-loop with cyclic-phosphate and hydroxyl ends, then separated labelled substrate and ligated product by denaturing polyacrylamide gel electrophoresis. Product analysis supported formation of a normal 3′,5′ phosphodiester bond at the joined site. This demonstrated a chemical activity; the initial paper treated broader physiological repair roles as proposals rather than as facts established for every organism.^[ref]

The labelling design gives an illuminating counting example. The reported broken substrate contained a labelled $19$-nucleotide strand and an unlabelled $20$-nucleotide partner. Joining them produces a $39$-nucleotide strand but does not double the number of labels per molecule.^[ref] If an invented measurement gives $30$ corrected label units in product and $70$ in unjoined labelled substrate, the inferred joined fraction is $30/(30+70)=0.30$, assuming equal recovery and label detection. Multiplying the product signal by $39/19$ would instead introduce an inappropriate length correction: the label counts molecules carrying that label, not their total RNA mass.

Tanaka's credited experiment exemplifies a productive move from a genomic association to a testable enzyme function. The observed chemical product supplies evidence that a neighboring-gene argument alone cannot provide.

Imaging newly emerging peptide chains at individual RNA molecules. Release and run-off controls help distinguish translation-dependent signals from aggregates or completed proteins.

Natallia Strushkevich is the first author of a 2011 structural study of the mitochondrial system that converts cholesterol toward pregnenolone. The team examined the cholesterol side-chain cleavage enzyme together with its electron-transfer partner adrenodoxin.^[ref]

An engineered fusion protein helped hold the partners together for crystal structure determination. The structure related the iron-sulfur cluster of adrenodoxin to the haem group of the catalytic protein, while structures with different bound sterols addressed successive reaction stages.^[ref]

The engineered connection was an experimental aid, not evidence that the native proteins form one continuous chain. Comparing fusion proteins with different linker lengths also tested how the imposed connection affected reduction of the catalytic partner.^[ref] The example connects a useful structure-stabilizing intervention to an explicit check on its functional consequences.

Ndt80 is a transcription factor in Saccharomyces cerevisiae that activates a set of genes needed for progression through meiosis and gametogenesis. It is encoded by the NDT80 gene. Its role links a developmental transition to coordinated gene expression, rather than to completion of a single structural event.

The initial 1995 study found that NDT80 gene mutants arrested at pachytene, a stage of meiotic prophase. Their homologous chromosomes remained joined by full-length synaptonemal complexes. Much of meiotic recombination still occurred, showing that chromosome exchange and progression out of this stage could be experimentally separated.^[ref]

A 1998 study then connected the phenotype to transcriptional control. Producing Ndt80 outside its normal developmental setting induced target genes, while the isolated protein bound a conserved upstream DNA sequence. The combination of altered gene expression and sequence binding supported a direct regulatory role.^[ref]

The NDT80 gene of budding yeast encodes Ndt80, a transcription factor involved in progression through meiosis. The gene is the DNA information; Ndt80 is the resulting regulatory protein. Keeping these distinct makes an intervention precise: deleting the NDT80 gene changes production of Ndt80, whereas measuring Ndt80 binding tests a property of the protein.

The original 1995 characterization found that NDT80 gene mutants arrested at pachytene with persistent synaptonemal complexes.^[ref] Subsequent experiments showed that Ndt80 bound upstream DNA and activated transcription of genes involved in meiotic division and reproductive cell formation.^[ref]

Negative-sense RNA is RNA whose sequence is complementary to the corresponding messenger RNA sequence. “Negative” specifies orientation relative to a coding message; it does not mean negative electric charge, damage, or lack of biological function. A negative-sense viral genome must first be copied into a message-compatible Positive-sense RNA before its encoded proteins can be made by translation.

For a short illustrative message $5^{\prime }\text{-AUGGCU-}{3}^{\prime }$, the complementary template is $3^{\prime }\text{-UACCGA-}{5}^{\prime }$, equivalently $5^{\prime }\text{-AGCCAU-}{3}^{\prime }$ when written in the conventional direction. The strands are complementary and antiparallel. Simply reversing the letters, without exchanging complementary bases, would not produce the negative-sense template. This small example shows why both sequence and direction matter.

The requirement creates a startup problem for a virus: if the entering genome cannot itself serve as messenger RNA, how can it make the enzyme needed to copy that genome? Vesicular stomatitis virus solves this by carrying an RNA-dependent RNA polymerase in its viral particle. In the 1970 experiment by D. Baltimore, A. S. Huang and M. Stampfer, virion preparations incorporated supplied ribonucleotide substrates into new RNA; the main product was complementary in sequence to the viral genome.^[ref]

This experiment connects a sequence classification to physical machinery packaged with the genome. Positive-sense RNA and Negative-sense RNA describe the relation of an RNA region to the coding message; identifying the sense does not by itself specify all details of genome segmentation, replication intermediates or transcription control.

Neil T. Hunt is a physical chemist who uses ultrafast infrared spectroscopy to study molecular structure and dynamics. His York profile describes applications of two-dimensional infrared spectroscopy to proteins, DNA and their interactions, together with instrument development at the Central Laser Facility.^[ref]

In two-dimensional infrared spectroscopy, a sequence of pulses distributes the response over two frequency axes. Diagonal and off-diagonal features reveal different information; correlations between vibrational modes can help distinguish structures whose ordinary absorption bands overlap. Hunt's account discusses this approach for proteins in water, where solvent absorption complicates observation of the protein bands.^[ref]

Hunt also coauthored the2022 RNA hairpin study using a rapid temperature jump followed by sufficiently fast cooling to observe refolding directly.^[ref]

The distinction is experimentally useful: an equilibrium spectrum records the population-weighted response after relaxation, while a time-resolved measurement follows how that response changes after a perturbation. Measuring the dynamics requires a known time reference and a sufficiently fast instrumental response, not merely a spectrum with narrow frequency bins.

A cell-surface protein whose phosphorylated intracellular region can recruit signalling adaptors.

In kidney podocytes, it is a component of the specialized filtration-slit architecture. Its intracellular signalling interactions can recruit Nck and actin-regulatory partners, connecting a membrane contact to cytoskeletal organization. ^[ref]

A syndrome characterized by substantial urinary protein loss with related changes such as low blood albumin and edema. It identifies a physiological pattern that can arise from several glomerular diseases.

Neuregulin 1 is a signaling protein ligand acting through ErbB receptors. The human NRG1 gene produces several protein isoforms through alternative promoter usage and alternative splicing; these products differ in their structure and tissue distribution.^[ref]

Its developmental roles include ventricular trabeculation. A targeted mutation in mice revealed that loss of neuregulin 1 disrupts normal development of several organ systems, providing experimental evidence of requirement rather than expression alone.^[ref]

Neuronal polarity is the structural and molecular differentiation of a neuron into compartments such as an axon and dendrites. Different distributions of proteins, transport machinery and synapses support different roles in receiving and sending signals. This organization does not require every electrical event to travel in only one direction: action potentials can propagate back into dendrites.

In 1988, Carlos G. Dotti, Christopher A. Sullivan and Gary A. Banker followed individual embryonic rat hippocampus neurons in culture using repeated photography and time-lapse imaging. Several initially similar neurites preceded rapid growth of one future axon; staining for microtubule-associated protein 2 helped distinguish later dendrites. Following the same biological cells over time directly tested the developmental sequence, which a collection of mature shapes could only suggest.^[ref]

Neutrophil elastase is a serine protease stored in granules of neutrophils. Its ability to cleave proteins can alter structures outside or within the cell, depending on where the active enzyme is located. A particularly illuminating example connects proteolysis to organization of chromatin.^[ref]

In a 2010 study, activation caused neutrophil elastase to reach the cell nucleus, where it partly degraded particular histones. Experiments with isolated nuclei and purified enzyme connected that cleavage to chromatin decondensation; Western blot measurements followed the protein changes. The study also found defective neutrophil extracellular trap formation in mice lacking the enzyme in its tested infection model.^[ref]

This separates several kinds of evidence. Observing a protein at a location is different from measuring its catalytic effects there. Combining localization, an enzyme assay and a loss-of-function comparison provides stronger mechanistic support than treating all three observations as equivalent.

A neutrophil extracellular trap is an extracellular web containing chromatin and antimicrobial proteins released by activated neutrophils. The DNA-containing fibers can bind microbes and concentrate associated defensive components outside the cell. This differs from phagocytosis, in which a cell engulfs a target into an intracellular compartment.^[ref]

The original 2004 report described fibers that bound both Gram-positive and Gram-negative bacteria, degraded virulence factors and killed bacteria in the tested system. The structural observation and the functional measurement answer different questions: an image can show a bacterium associated with a web, while a viability assay tests whether the bacterium survives.^[ref]

A useful experimental comparison would measure trapping and survival separately, then test whether disrupting the DNA scaffold changes either endpoint. Such an intervention needs controls for effects on bacteria and neutrophils themselves. This is an illustrative design principle, not an additional protocol or numerical result attributed to the 2004 abstract.

The name describes a released structure; it does not by itself identify the complete pathway of release, establish that every neutrophil forms one, or prove that every trapped microorganism is killed. Distinguishing the web, its cellular production and its consequences keeps a morphological observation from becoming an unsupported universal mechanism.

NhaA is a sodium/proton antiporter exemplified by the Escherichia coli membrane protein. It couples the movement of sodium ions to proton movement in the opposite direction across a cell membrane, contributing to ion and pH regulation. The name of this particular protein should not be confused with every sodium/proton exchanger.

A 1993 experiment purified NhaA and placed it in sodium-loaded proteoliposomes: artificial membrane vesicles containing the transport protein. Parallel sodium-efflux and proton-influx measurements supported two protons per sodium ion over the tested pH range 7.2–8.1. A second determination used membrane electric potential difference and equilibrium gradients, under assumptions of coupled transport.^[ref]

For an illustrative cycle with two protons entering and one sodium ion leaving, the inward transfer of electric charge is $2e-e=e$, where $e$ is the elementary charge. Reversing the cycle reverses that transfer. Opposite transport directions therefore do not imply electrical neutrality, nor do they alone determine which direction is energetically favored; the electrochemical gradients matter.

A 2005 X-ray crystallography study supplied a different kind of evidence: a structure of downregulated NhaA, including a cytoplasm-facing funnel toward a putative ion-binding region. The authors proposed a mechanism in which access changes between the two sides. A static structure helps constrain such a mechanism but does not directly measure the transported ratio or film a working exchange cycle.^[ref]

Researcher in evolution and genome organization. Irwin and collaborators investigated whether viral proteins contributed to histone depletion in dinoflagellates, testing a possible evolutionary explanation for unusual chromosome packaging.^[ref]