Nexin can be located on this cross-section of an axoneme


TTF-1 needs to have nuclear staining on immunohistochemistry to count as positive. Cytoplasmic staining is disregarded for diagnostic purposes. [ 10 ]


Micrograph  of a metastatic lung adenocarcinoma (found in the brain) that exhibits nuclear staining (brown) for  TTF-1 .


Dimer of the Influenzavirus A non-structural protein 1 from A/Vietnam/1203/2004(H5N1)


A  nucleosome  is a combination of  DNA  +  histone proteins .


Cross-sectional drawing of the  Ebola virus  particle, with structures of the major proteins shown and labelled on the right


OCC-1 Phylogenetic Tree


MSA for the Occludin/ELL Domain in OCEL1 and its five human paralogs. The beginnings and ends of each paralog were trimmed.


Tertiary structure of the human OCEL1 protein as predicted by iTASSER. [ 14 ] [ 15 ]


RNA folding of the 3’ UTR in OCEL1 generated with RNAfold Web Server. [ 27 ]


In human, the OCA2 gene is located on the long (q) arm of  chromosome 15  between positions 12 and 13.1


Figure 1. RNA polymerase II elongation control.  Pol II comes under the control of negative elongation factors (DSIF and NELF) shortly after initiation. P-TEFb mediates a transition into productive elongation by phosphorylating the two negative factors and the polymerase and is regulated by association with the 7SK snRNP.


Figure 2. Structure of P-TEFb bound by HIV Tat.  PDB ID: 3MIA Cdk9 (blue), cyclin T1 (cyan), Tat (orange), ATP (magenta), magnesium (purple), zinc atoms (yellow).


Figure 3. Reversible association of P-TEFb with the 7SK snRNP.  P-TEFb is released from the 7SK snRNP by Brd4 or HIV Tat. HEXIM is ejected and the two proteins are replaced by hrRNPs. The reverse of this process requires other unknown factors.


p53 pathway : In a normal cell, p53 is inactivated by its negative regulator, mdm2. Upon DNA damage or other stresses, various pathways will lead to the dissociation of the p53 and mdm2 complex. Once activated, p53 will induce a cell cycle arrest to allow either repair and survival of the cell or apoptosis to discard the damaged cell. How p53 makes this choice is currently unknown.


Activation of p53 in response to stress signals initiates its transcriptional activity, leading to the activation of cellular protective pathways [ 25 ]   p53 binds to the DNA in a tetrameric configuration and promotes the transcription of a wide array of genes. Pictured are key p53 pathways and transcriptional targets regulated by p53 with a specific emphasis on p53-dependent DNA repair genes. BER (base excision repair), NER (nucleotide excision repair), MMR (mismatch repair), HR (homologous recombination), NHEJ (non-homologous end-joining), DDR (DNA damage repair)


An overview of the molecular mechanism of action of p53 on the angiogenesis [ 39 ]


Overview of signal transduction pathways involved in  apoptosis


A  micrograph  showing cells with abnormal p53 expression (brown) in a brain tumor.  p53 immunostain .


Immunohistochemistry  for p53 can help distinguish a  papillary urothelial neoplasm of low malignant potential  (PUNLMP) from a low grade  urothelial carcinoma . Overexpression is seen in 75% of low-grade urothelial carcinomas and only 10% of PUNLMP. [ 63 ] [ 64 ]


Pathogenic mechanisms associated with p53 mutations [ 68 ]  (A) The wild-type response of p53 involves the formation of homotetramers, which regulate gene expression at p53 responsive elements. (B) In contrast, the dominant-negative effect of p53 mutants occurs through the formation of heterotetramers. These heterotetramers, composed of both p53 wild-type and p53 mutant monomers, lack transcriptional ability. This dominant- negative mechanism can manifest in conditions of heterozygosity, where a p53 wild-type allele coexists with a p53 mutant allele (p53mut/+). (C) Loss- of-function is characterized by the absence of p53 wild-type expression and the lack of any form of activity by the p53 mutant protein. This typically occurs when all p53 alleles are inactivated. (D) Gain-of-function involves the acquisition of neomorphic activities by p53 mutant proteins. These neomorphic activities are often described as the hijacking of additional transcriptional factors, indirectly influencing gene regulation and resulting in pro-tumorigenic phenotypes. Abbreviation: WT, wild type. [ 68 ]


A schematic of the known protein domains in p53 (NLS = Nuclear Localization Signal)


Crystal structure of four p53 DNA binding domains (as found in the bioactive homo-tetramer)


Ripple chocolate pea milk


Oubli ( Pentadiplandra   brazzeana)  Found in Tropical West Africa [ 5 ]


Illustration of sweet-tasting proteins, regardless of their extraction origin, source, and types. [ 8 ]


Illustration showing the binding of a peptide hormone to the cell


Location of human  PGLYRP3  gene on chromosome 1 and schematic gene, cDNA, and protein structures with exons, introns, and protein domains indicated.


Location of human  PGLYRP4  gene on chromosome 1 and schematic gene, cDNA, and protein structures with exons, introns, and protein domains indicated.


Schematic illustration of the evolution of the MACPF–tachylectin complex in ampullariids. Based on the genomic arrangements of the MACPF and tachylectin genes, the model proposes that a single copy of MACPF–tachylectin complex was present in the common ancestor of ampullariids. Only in the two species of Pomacea has it become highly diversified, with both MACPF-tachylectin genes that are conserved across Ampullariidae, and multiple  Pomacea  specific MACPF-tachylectin genes that were generated by tandem duplication. The final 1-MACPF and 2-tachylectin configuration is exclusively expressed in the albumen gland of  Pomacea  and the proteins detected in their eggs. Numbers below and inside gene diagram boxes are scaffold numbers and gene numbers in the scaffold, respectively. For instance,  Lanistes nyassanus  contains a MACPF gene (Lny_22924_0.25) and a tachylectin gene (Lny_22924_0.27) in scaffold Lny_22924. For  Pomacea canaliculata , the chromosome numbers are shown above the gene diagram boxes. More details can be found in Sun et al., 2019. [ 8 ]


This image depicts the various types of mushrooms within the  Amanita  genus. Phallolysin is most commonly found in the  Amanita phalloides  species.


Image depicting the basis of cytolysis, in which an external factor causes an influx of water causing the volume of the cell to exceed the allowed capacity, further causing it to rupture, or lyse, and expel the internal cellular components.


APS and Ru(Bpy) 3  reaction to produce excited Ru(Bpy) 3


Formation of covalent bond between amino acid side chains (Tyrosine)


Camera apparatus used to irradiate the protein mixture


The marine worm  Chaetopterus  was the source of the first photoprotein to be discovered.


Phycobiliproteins  (like phycoerythrin) usually form rods of stacked disks in  phycobilisomes . [ 6 ]


The crystal structure of B-phycoerythrin from  red algae   Porphyridium cruentum  ( PDB  ID: 3V57  [ 9 ] [ 10 ] [ 11 ] ). The asymmetric unit ( α β ) 2  on the left and assumed biological molecule ( α β ) 3 . It contains  phycoerythrobilin ,  N -methyl asparagine  and  SO 2− 4 .


Phycoerythrobilin is the typical chromophore in phycoerythrin. It is similar to  porphyrin  of  chlorophyll  for example, but  tetrapyrrole  is linear, not closed into ring with metal ion in the middle.


The  red algae   Gracilaria  contains R-phycoerythrin.


The crystal structure of phycoerythrin 545 (PE545) from a  unicellular   cryptophyte   Rhodomonas  CS24 ( PDB  ID: 1XG0  [ 13 ] [ 14 ] [ 11 ] ). Colors: chains –  alpha-2 ,  alpha-3 ,  beta ,  beta  ( helixes ,  sheets  are yellow),  phycoerythrobilin ,  15,16-dihydrobiliverdin  (15,16-DHBV),  5-hydroxylysine ,  N -methyl asparagine ,  Mg 2+ ,  Cl − .


The crystal structure of R-phycoerythrin from  red algae   Gracilaria chilensis  ( PDB  ID: 1EYX  [ 15 ] [ 16 ] [ 11 ] ) - basic  oligomer  ( α β γ ) 2  (so called asymmetric unit). It contains  phycocyanobilin ,  biliverdine IX alpha ,  phycourobilin ,  N -methyl asparagine ,  SO 4 2− . One fragment of γ chain is red, second one white because it is not considered as  alpha helix  despite identical aminoacid sequence.


The entire  oligomer  of R-phycoerythrin from  Gracilaria chilensis  ( α β γ ) 6   ( PDB  ID: 1EYX  [ 15 ] [ 16 ] [ 11 ] )


Absorption (or extinction) and fluorescent (or emission) spectra of phycoerythrin


Excitation and emission profiles for R-Phycoerythrin from two different algae. Common laser excitation wavelengths are also noted.


The piwi domain of an  argonaute  protein with bound  siRNA , components of the  RNA-induced silencing complex  that mediates  gene silencing  by  RNA interference .


All human Piwi proteins and  argonaute  proteins have the same RNA binding domains, PAZ and Piwi. [ 2 ]


Piwi-piRNA interactions: Within the nucleus, this pathway is involved in  DNA methylation  (A), histone methylation of H3K9 through interactions with  heterochromatin protein 1  (HP1) and H3K9  histone methyltransferase  (B). The Piwi-piRNA pathway also interacts with the elF translational initiator (C). [ 3 ]


A solution phase representation of pGSN in the presence of Ca 2+  adapted from  3FFN  and low-resolution  SAXS  information. [ 12 ]  The 24 AA N-terminal extension unique to the plasma isoform was manually added (left, light blue); no structural information for it is known nor represented. Colors represent the six domains of Gelsolin. [ 13 ] [ 14 ]


The outer layer of  trophoblast  cells invade the  endometrium


Preimplantation factor deactivates p53, preventing apoptosis


PrP Sc  (stained in red) revealed in a photomicrograph of scrapie-infected mouse neuronal cells.


Models of normal (PrP C ) and infectious (PrP Sc ) forms of prion protein on a membrane: polypeptide (turquoise); glycans (red); glycolipid anchors (blue). The core structures are based on NMR spectroscopy (PrP C ) and cryo-electron microscopy (PrP Sc ).


Heterodimer model of prion propagation


Fibril model of prion propagation.


Predicted tertiary structure of PROB1 generated by I-Tasser [ 11 ]  and rendered in PyMOL. [ 12 ]  The dark blue indicates prolines and yellow marks the DUF. The alpha helices are colored green, beta sheets are colored light blue, and random coils are colored pink.


A subset of the mammalian orthologs of PROB1 predicted by BLAST.


Cryo-EM structure of the DNA-bound PolD–PCNA processive complex


The evolutionary history of  PROSER2  versus Cytochrome C and Fibrinogen alpha subunit. Each data point on the graph represents a homolog of the human gene found in a different species that was found using a BLAST search. This search resulted in percent identities which are graphed against the estimated time of divergence from humans which was found using TimeTree.This graph demonstrates that  PROSER2  is a fast-evolving gene, similar to the Fibrinogen alpha subunit. [ 25 ] [ 26 ]


Human PROSER2 protein internal structure and features. [ 6 ] [ 30 ] [ 31 ]


Cartoon representation of a proteasome. Its active sites are sheltered inside the tube (blue). The caps (red; in this case, 11S regulatory particles) on the ends regulate entry into the destruction chamber, where the protein is degraded.


Top view of the proteasome above.


Schematic diagram of the proteasome 20S core particle viewed from one side. The α subunits that make up the outer two rings are shown in green, and the β subunits that make up the inner two rings are shown in blue.


Cartoon representation of the 26S proteasome. [ 30 ]


Three distinct conformational states of the 26S proteasome. [ 37 ]  The conformations are hypothesized to be responsible for recruitment of the substrate, its irreversible commitment, and finally processing and translocation into the core particle, where degradation occurs.


Ribbon diagram  of  ubiquitin , the highly conserved  protein  that serves as a molecular tag targeting proteins for degradation by the proteasome


The  ubiquitination  pathway


A cutaway view of the proteasome 20S core particle illustrating the locations of the  active sites . The α subunits are represented as green spheres and the β subunits as protein backbones colored by individual  polypeptide chain . The small pink spheres represent the location of the active-site  threonine  residue in each subunit. Light blue chemical structures are the inhibitor  bortezomib  bound to the active sites.


The assembled complex of  hslV  (blue) and  hslU  (red) from  E. coli . This complex of  heat shock proteins  is thought to resemble the ancestor of the modern proteasome.


Chemical structure of  bortezomib  (Boronated form of MG132), a proteasome inhibitor used in  chemotherapy  that is particularly effective against  multiple myeloma


Bortezomib  bound to the core particle in a  yeast  proteasome. The bortezomib molecule is in the center colored by atom type ( carbon  = pink,  nitrogen  = blue,  oxygen  = red,  boron  = yellow), surrounded by the local protein surface. The blue patch is the catalytic  threonine  residue whose activity is blocked by the presence of bortezomib.


This process flow diagram shows how monoclonal antibodies are typically purified at industrial scale.


Pasteurized milk being held in bulk heating tank for cheese making.


Composition of solids (non-water elements) in milk


Mechanism of denaturing protein adsorption


Basic mechanism of enzyme action


Protein biosynthesis starting with transcription and post-transcriptional modifications in the nucleus. Then the mature mRNA is exported to the cytoplasm where it is translated. The polypeptide chain then folds and is post-translationally modified.


Illustrates the conversion of the template strand of DNA to the pre-mRNA molecule by RNA polymerase.


Outlines the process of post-transcriptionally modifying pre-mRNA through capping, polyadenylation and splicing to produce a mature mRNA molecule ready for export from the nucleus.


Illustrates the translation process showing the cycle of tRNA codon-anti-codon pairing and amino acid incorporation into the growing polypeptide chain by the ribosome.


A ribosome on a strand of mRNA with tRNA's arriving, performing codon-anti-codon base pairing, delivering their amino acid to the growing polypeptide chain and leaving. Demonstrates the action of the ribosome as a  biological machine  which functions on a  nanoscale  to perform translation. The ribosome moves along the mature mRNA molecule incorporating tRNA and producing a polypeptide chain.


Shows the process of a polypeptide chain folding from its initial primary structure through to the quaternary structure.


Shows a post-translational modification of the protein by protease cleavage, illustrating that pre-existing bonds are retained even if when the polypeptide chain is cleaved.


Shows the post-translational modification of protein by methylation, acetylation and phosphorylation


Illustrates the difference in structure between N-linked and O-linked glycosylation on a polypeptide chain.


Shows the formation of disulphide covalent bonds as a post-translational modification. Disulphide bonds can either form within a single polypeptide chain (left) or between polypeptide chains in a multi-subunit protein complex (right).


A comparison between an unaffected individual and an individual with sickle cell anaemia illustrating the different red blood cell shapes and differing blood flow within blood vessels.


Formation of cancerous genes due to malfunction of suppressor genes.


Arginine methylation by type I and II PRMTs


Lysine methylation by PKMTs and demethylation by PKDMs


Crystallographic structure  of  cytochrome P450  from the bacteria  S. coelicolor  (rainbow colored cartoon,  N-terminus  = blue,  C-terminus  = red) complexed with  heme  cofactor (magenta  spheres ) and two molecules of its endogenous substrate epi-isozizaene as orange and cyan spheres respectively.  The orange-colored substrate resides in the  monooxygenase  site while the cyan-colored substrate occupies the substrate entrance site. An unoccupied moonlighting  terpene   synthase  site is designated by the orange arrow. [ 1 ]


Crystallographic structure of aconitase [ 18 ]


A  crystallin  from ducks that exhibits  argininosuccinate lyase  activity and is a key structural component in eye lenses, an example of gene sharing


The mechanism of protein splicing involving inteins. In this scheme, the N-extein is shown in red, the intein in black, and the C-extein in blue. X represents either an oxygen or sulfur atom.


Intein splicing occurs post-translationally in a self-catalytic process. Here, the extein is shown in red and the intein in blue. Image created with Biorender.com.


Crystal structure  of W741L  mutant   androgen receptor   ligand-binding domain  and  ( R )-bicalutamide  complex. [ 1 ]  An example of a protein–ligand complex.


These are examples of  membrane receptors . Typically, they are proteins that are embedded in the membrane. Although there are many different ligands located outside of the cell, membrane proteins are specific, and only certain ligands will bind to each one. That is why each protein has a different ligand, and also induces a different cellular response. The response may be  transcription  of a gene, cell growth, or many other cellular actions.


Amino acids are the building blocks of protein.


Amino acids are necessary nutrients. Present in every cell, they are also precursors to nucleic acids, co-enzymes, hormones, immune response, repair and other molecules essential for life.


Protein milkshakes, made from protein powder (center) and milk (left), are a common  bodybuilding supplement


An education campaign launched by the  United States Department of Agriculture  about 100 years ago, on  cottage cheese  as a lower-cost protein substitute for meat.


Average protein supply by region and origin


A child in Nigeria during the  Biafra War  with  kwashiorkor  – one of the  three protein energy malnutrition ailments  affecting over 10 million children in developing countries. [ 58 ]


Location of PRR29 gene relative to its neighbors


Locus of PRR29 [ 11 ]


Genomic view of PRR29


3D structure of PRR29 protein


3D structure prediction from I-TASSER  [ 26 ]


Expression data for PRR29 based on RNA sequencing of human tissue samples


Expression data for PRR29 from Illumina bodyMap 2 transcriptome


A table comparing the divergence of PRR29 in different species relative to the human gene.


PRR29 Expression [ 27 ]


PRR29 Unrooted Phylogenetic Tree [ 39 ]


PRR29's rate of mutation compared to that of cytochrome c and fibrinogen alpha


Retinol-binding protein (plasma), Human.


Figure 1:  A sequence logo constructed from the 13-nucleotide repeat regions found by EBI-RADAR, showing a clear TxTxTxT binding motif embedded within these regions.


Some of the signalling events involving rsk.


Domain structure of rsk. Numbers refer to amino acid residues of p90 rsk-1 from rat. [ 6 ]


A comparison of the similar structures of abrin-a (red) and ricin (blue)


Castor beans


Castor oil seeds in the Royal Botanic Gardens, Kew Economic Botany Collection


A metal vial containing ricin from the  2003 ricin letters


Ricin toxin, RiVax, RTA1-33/44-198, and a single domain antibody-antigen complex with the RTA1-33/44-198 immunogen. Original figure can be found in Legler, et al.  [ 57 ] [ 58 ]


Function of RNA polymerase II (transcription). Green: newly synthesized RNA strand by enzyme


RNA polymerase II of  Saccharomyces cerevisiae  consisting of all 12 subunits. [ 4 ]


Eukaryotic RNA-polymerase II from  Saccharomyces cerevisiae , PDB ID. [ 9 ]  Subunits colored:   RPB3 – orange  ,   RPB11 – yellow  ,   RPB2 – wheat ,   RPB1 – red ,   RPB6 – pink , the rest 7 subunits are colored gray.


RNA Polymerase II gray. Alpha-amanitin interaction (red).


The hypothesized transition from RNA to proteins to DNA


ColE1 replication control


RuvA-RuvB complex heteromer, Thermus thermophilus


SAAL1 gene neighborhood at loci 11p15.1 [ 8 ]


SAAL1 mRNA sequence and translated amino acid sequence. Exon boundaries, start and stop codons, motifs, and post-translational modifications are annotated. Well conserved base pairs and amino acids are bolded


I-TASSER generated model of SAAL1 tertiary structure. The N-terminus is blue and C-terminus is red. [ 18 ] [ 19 ] [ 20 ]


Three page PDF of multiple sequence alignment of vertebrate SAAL1 orthologs referenced in the orthologs table. [ 22 ] [ 48 ]


Two page PDF of multiple sequence alignment of invertebrate and non-metazoan SAAL1 orthologs in the table, excluding the fungi orthologs. Poorly aligned regions are not shown. [ 22 ] [ 48 ]


SAAL1 evolutionary rate vs fibrinogen alpha and cytochrome c.


Biological assembly of SHOC2 protein as shown by crystal structure to a resolution of 2.4 Angstrom. Sulfate molecules are labeled purple. Structure from 10.2210/pdb7TVG/pdb.


SHOC2 protein leucine rich domain. Leucine amino acids shown as bright orange sticks.


An image of the secondary structure of an H/ACA box  snoRNA  transcript.  This  RNA  transcript forms a class of protein-RNA complexes called H/ACA box  snoRNPs .  Shq1p is believed to interact with these  snoRNP  complexes.


Fig. 1  The diagram shows the role of Sic1 in Clb5,6-Cdk1 inhibition and its phosphorylation-mediated polyubiquitination and destruction. Destruction allows for Clb5,6-Cdk1 activity and S-phase entry.


Fig. 2  The first step of the degradation of Sic1 is its phosphorylation by Cdc28-Cln followed by the degradation through SCF.


Fig. 3  Sic1 protein distinguished by different protein chains. The protein has disordered regions, allowing it to be a useful tool in studying and manipulating phosphorylation sites.


Fig. 4  Sic1 Phosphorylation Mechanism 1.  In mechanism 1, Koivomagi proposes that the phosphorylated primary site immediately shifts over to another location so that another CDK site can be phosphorylated during the same binding event.


Fig. 5  Sic1 Phosphorylation Mechanism 2. Koivomagi proposes that phosphorylated primary site does not dissociate from the complex so that the intermediate CDK sites are sequentially phosphorylated in a single binding event.


Catecholate -iron binding.  A typical complex would exhibit three such interactions.


Enterobactin , a catecholate siderophore


Diagram of the SKIDA1 protein.


A predicted 3D structure of SKIDA1. The Ski/Sno/Dac domain, DUF4584, and C-Terminal region (amino acids 844-908) are annotated.


SKIDA1 is highly expressed in  Purkinje cells  in the cerebellum.


Expression of SKIDA1 in the house mouse fetal heart increases, then decreases with age.


Fig.1. Structures of the Maf family proteins.


Fig. 2. Amino acid sequence alignments of human sMafs.


Fig.3 Binding motifs recognized by CNC/Bach and sMafs.


Location of SMCO3 on Chromosome 12.


Predicted stem-loop structure of the 5' UTR of SMCO3.


Predicted structure of SMCO3 created using iTasser and PYMOL.


Comparison of protein amino acid sequence divergence and time of divergence as measured by million years to most recent common ancestor (MRCA). Corrected % sequence divergence (m) is measured with respect to the human sequence. CYCS [cytochome C], FGA [fibrinogen alpha chain], SMCO3 [single-pass membrane and coiled-coil domain-containing protein 3].


A table with accession number,  chromosome  location, strand location, size, and known aliases.


Conceptual Translation of SMIM23. Labeled are the start and stop codon, exon splice sites,  polyadenylation signal  as well as singly conserved based highlighted in yellow, alpha helices with arrows, transmembrane domain in purple, domains of unknown function in blue, and a repeat domain is underlined.


Schematic of protein. Marking locations of notable features that were confirmed with some level of confidence. Here red stands for phosphorylation site and grey stands for C-terminal GPI-modification site. The transmembrane domain in relation to the rest of the protein is shown.


Predicted structure of SMIM23 by I-Tasser program.


A phylogenetic tree of the SMIM23 gene in various animals as seen in the table included. Abbreviations refer to the different common names i.e. Hu SMIM23 refers to the human gene.


Fluorescent proteins visualize the cell cycle progression.  IFP2.0-hGem(1/110) fluorescence is shown in green and highlights the S/G 2 /M phases. smURFP-hCdtI(30/120) fluorescence is shown in red and highlights the G 0 /G 1  phases.


Image shows  E. coli  expressing smURFP, pelleting of  E. coli , removal of media,  E. coli  lysis, smURFP binding to NiNTA, smURFP elution, and buffer exchange.


The small Ultra-Red Fluorescent Protein (smURFP) is a self-labeling protein. The substrate is fluorogenic, fluoresces when attached, and quenches fluorescent cargo. The smURFP-tag [ 20 ]  has novel properties for tool development.


smURFP was genetically fused to human, lamin B1 to show the nuclear envelope with fluorescence.  Localization of the Lamin B1 protein changes during different phases of the cell cycle.


smURFP expressed in neuronal culture does not show aggregation in lysosomes, which was seen with the fluorescent protein,  mCherry .


Far Red & Near Infrared FUCCI visualizes the birth of a multinucleated cell, which is common in many cancer cells.


smURFP (light-blue) expressed in  E. coli .


C1orf142 model as proposed by I-Tasser. Image colored in rainbow from N to C terminus.


Example of SNAP25 SNARE acrivity resulting in neurotransmitter release of Ca 2+ .


Diagram of yeast signaling pathways in response to glucose. Solid arrows represent transformations and/or translocations and dotted lines represent regulatory or catalytic influences.


Snf3/Rgt2-singalling pathway. In absence of glucose repressing complex composed of Rgt1, Mth1/Std1, Cyc8 and Tup1 blocks transcription of HXT genes. When glucose (Glu) is present casein kinase is activated and phosphorylates Mth1/Std1 which is subsequently ubiquitinated and degraded by the proteasome allowing transcription to proceed.


The putative topology of yeast Snf3. The C-terminal extension is not shown in its complete size. In reality it comprises 303 of the 845 residues.


Tertiary structure of the SNX9 which gives an idea of the tertiary structure of the SNX8, since primary structure shares 20% sequence identity and 0.3 sequence similarity with SNX8 primary structure. [ 1 ]


SNX8 primary structure highlighting relevant domains and amino acids. [ 2 ] [ 4 ] [ 5 ]


Simplified scheme of DNA-triggered SNX8-mediated association of MITA and VPS34, and its intracellular transport pathway from RE to perinuclear microsomes via Golgi apparatus. [ 10 ]


Simplified scheme of SNX8 participation in the IFNγ-triggered IKKβ-mediated noncanonical signaling pathway (autophosphorylation not shown). [ 5 ]


Simplified scheme of APP traffic and its amyloidogenic and non-amyloidogenic proteolytic degradative pathways [ 12 ]


This bar plot shows the proportion of tumor samples from 15 cancer types that have any kind of altering mutation(s) in the given protein. [ 20 ]


A diagram of the structure of spidroin


Ideogram of the SPMIP10 Gene Location on Chromosome 5. The gene location is indicated by the red line.


SPMIP10 predicted tertiary structure. Generated using AlphaFold.


SPMIP10 predicted tertiary structure. Generated using iTasser.


SPMIP10 Microarray Expression Schematic in the Human Brain. Yellow boxes indicate areas of dense expression in the posterior lobe. Data obtained from the Allen Brain Atlas website.


SPMIP10 Transcription Regulation Diagram. Two predicated enhancers (E2405703 and E2405704) and an initiation region (Tex43_1) are labeled.


Annotated Conserved Post-translational Modifications for SPMIP10 Diagram. Longer ticks indicate higher confidence scores.


Graph 1: Corrected sequence divergence vs estimated date of divergence for SPMIP10, Cytochrome C and Fibrinogen Alpha.


Solution structure  of the  RRM  domain of the mouse SR protein  Sfrs9  based on  1wg4 .


SR proteins translocating out of the nucleus with TAP


STAT5 activation.


Domains of STAT proteins


Localization of Staufen (Stau:GFP) in Drosophila stage 9 oocytes (white arrow).


Cartoon representation of the molecular structure of SpeA1.


Structure of SpeB.


Structure of SpeA1.


T-cell dependent b-cell activation, showing TH2-cell (left) B-cell (right) and several interaction molecules.


T-cell receptor .


SUMO  enzymatic  cascade


Structure schematic of human SUMO1 protein made with  iMol  and based on PDB file 1A5R, an NMR structure; the backbone of the protein is represented as a ribbon, highlighting secondary structure; N-terminus in blue, C-terminus in red


The same structure, representing atoms as spheres, shows the shape of the protein; human SUMO1, PDB file 1A5R


This representation of SUMOylation regulation as described in the 2024 publication by Gutierrez-Morton et al. illustrates how some of the multiple inhibitory mechanisms interact to regulate foundational aspects of cell biology. Produced with Biorender.


SELDI Mechanism


Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis


Neurons were grown in tissue culture and stained with antibody to  MAP2  protein in green and MAP tau in red using the  immunofluorescence  technique. MAP2 is found only in dendrites and perikarya, while tau is found not only in the dendrites and perikarya but also in axons. As a result, axons appear red while the dendrites and perikarya appear yellow, due to superimposition of the red and green signals. DNA is shown in blue using the  DAPI  stain which highlights the nuclei. Image courtesy  EnCor Biotechnology Inc .


Corticogenesis in wild-type mice. Similar neuronal migration occurs in humans in the development of the six-layered cerebral cortex.


Corticogenesis in reeler mutant mice. Tbr-1 mutation results in similar abnormalities in cortical migration through reduction of Reelin expression.


A diagram from NCBI showing TEDC2 and its gene neighborhood on chromosome 16.


A table showing which exons are found in the 6 TEDC2 isoforms. Green = contains a start codon. Red = contains a stop codon. Check = Exon included in the final mRNA transcript. -- = exon is excluded from the final mRNA transcript. U = exon is present but is untranslated.


The predicted TEDC2 tertiary structure model of highest probability, generated by I-TASSER. [ 20 ]


Graphical representation of TEDC2 showing domains and modification sites, created with DOG. [ 21 ]


Structure of tetanospasmin


Mechanism of action of tetanospasmin


The formation of the  sorbitol dehydrogenase  tetramer from its monomers via dimers.


A homotetrameric complex,  beta-glucuronidase  (a  glycosidase ). Each subunit has the same  amino acid  sequence.


The heterotetrameric molecule  haemoglobin , made up of four subunits of two different types (coloured  red  and  blue .)


Expression of TEX9 in human tissue samples


TEX9 isoform 1 with phosphorylation (orange) and ubiquitylation (blue) sites. The structure has 99% confidence and 98% coverage. [ 10 ]


TEX9's mutation rate compared to fibrinogen, beta-globin, and cytochrome c.


Unrooted phylogenetic tree of TEX9 orthologs. Branch length represents relative evolutionary distance between organisms.


Gene neighborhood of TEX36 from  NCBI , gene database. Genes ALDOAP2, or  aldolace, fructose-biphosphate A2 , and other uncharacterized loci LOC105378547 and LOC107984277 are in the environment of TEX36, located on chromosome 10,  open reading frame  22. [ 1 ]


Schematic of identified domains and motifs along with post-translational modifications of TEX36.  These include  amidation  sites where there are brackets, the  MAPK  interacting motif, and HDNR motif.  Red flags represent  casein kinase  phosphorylation sites, pat4 nuclearlization signals with grey flags, and  protein kinase c  phosphorylation sites with green lines. [ 9 ]


Predicted secondary structure of TEX36 including several alpha helices and beta strands, created with i-Tasser. [ 12 ]


Unrooted phylogenetic tree based on alignment data of TEX36 protein, including 10 orthologs of the protein. [ 27 ]


Structure of  alpha-bungarotoxin  (blue) in complex with the alpha-9 nAChR subunit (orange), showing interactions with loops I and II [ 19 ]


View of human  TMED5  gene isoform 1 and 2 with promoter and exon locations.


Conceptual translation of TMED5. Labeled are the start and stop  codon , exon splice sites, domains and motifs,  polyadenylation  signals, predicted RNA and miRNA binding proteins, and predicted  post-translational modifications . Bolded amino acids and nucleotides represent highly conserved amongst distant orthologs.


TMED5 protein isoform 1 visual made via Protter. [ 15 ]


TMED5 protein isoform 2 visual made via Protter. [ 15 ]


Predicted tertiary structure of TMED5 generated by Phyre2. [ 20 ]  Signal peptide is highlighted in yellow. GOLD domain in the lumen is shown to be made up of beta sheets. Transmembrane domain is grayed out followed by the short cytosolic sequence.


TMED5 evolutionary graph shows evolutionary rate.  Cytochrome C  is shown to represent a slow-evolutionary rate and  Fibrinogen alpha  represents a fast-evolutionary rate. TMED5 is shown to have a fast-evolutionary rate similar to Fibrinogen alpha. Estimated date of divergence for paralogs were plotted: TMED1 diverged ~64 million years ago (MYA), TMED3 diverged ~118 MYA, and TMED7 diverged ~122 MYA.


Human chromosome 1


TMEM125 predicted topology, generated by Phyre2


TMEM125 domains and predicted sites of post-translational modifications (PTMs)


List of TMEM125 orthologs


Conceptual translation of Transmembrane Protein 144 mRNA transcript sequence with peptide sequence. DNA annotations mark an upstream in-frame stop codon, start codon, exon borders, stop codon, polyadenylation signals, and polyadenylation sites. Protein annotations mark the ten transmembrane domain regions, internal repeats, and the region of the protein excluded from the second isoform. Amino acids conserved in distant orthologs are bolded.


Predicted tertiary structure of human transmembrane protein 144. Regions of dark blue are very high confidence, light blue regions are confident, yellow regions are low confidence, and orange regions are very low confidence.


Transmembrane Protein 144 schematic with transmembrane domains and predicted post translational modifications. P indicates predicted sites of phosphorylation. SUMO indicates a predicted sumoylation site.


Multiple sequence alignment of human Transmembrane Protein 144 with vertebrate orthologs. Some amino acids in the ortholog sequences were cut out at the N-terminus. Amino acids are highlighted by shared properties and structure. Consensus sequences denote highly conserved amino acids with a capital letter, moderately conserved amino acids with a lowercase letter, and low conservation with a dot. A plus or minus symbol in the consensus sequence indicates conserved basic (+) or acidic (-) properties. Transmembrane regions are boxed in orange and exon boundaries are marked in pink.


Multiple sequence alignment of human Transmembrane Protein 144 to invertebrate orthologs. Consensus sequences denote highly conserved amino acids with a capital letter, moderately conserved amino acids with a lowercase letter, and low conservation with a dot. A plus or minus symbol in the consensus sequence indicates conserved basic (+) or acidic (-) properties. Transmembrane regions are boxed in orange and exon boundaries are marked in pink.


Location of TVP23A on Chromosome 16 (red line)


Protein structure of TVP23A as predicted by iTASSER


A generic transcription factory during transcription, highlighting the possibility of transcribing more than one gene at a time. The diagram includes 8 RNA polymerases however the number can vary depending on cell type. The image also includes transcription factors and a porous, protein core.


The hypothesis that it is the transcription factory that remains immobilised during transcription as opposed to the DNA template. It shows how a section of the gene being transcribed (brown) gets pulled and shuttled through the  RNA polymerase  during the process.


The attraction of related genes to RNAP and the required transcription factors causes the formation of a chromatin loop, thereby affecting the genome structure


Surface representation of ubiquitin


The ubiquitylation system (showing a RING E3 ligase)


Glycine and lysine linked by an isopeptide bond. The isopeptide bond is highlighted yellow.


Diagram of lysine 48-linked diubiquitin . The linkage between the two ubiquitin chains is shown in orange.


Diagram of lysine 63-linked diubiquitin . The linkage between the two ubiquitin chains is shown in orange.


Ligands for different VEGF receptors. [ 4 ] [ 5 ]


The  helix bundle  in the headpiece domain of  chicken  villin.


Surface model of the WAVE regulatory holocomplex displaying all five of its components in heteropentameric form.


Figure 1. Bird's Eye View of the ZNF226 Transcript and Promoters


Figure 2. Human ZNF226 5’ UTR Secondary Structure


Figure 3. Human ZNF226 3' UTR Secondary Structure


Figure 4. A multiple sequence alignment of human ZNF226 and ortholog species with selected regions highlighted.


Figure 5. A multiple sequence alignment of human ZNF226 and ortholog species with selected regions highlighted.


Figure 6. The ZNF226 evolutionary rate in comparison to the cytochrome c and fibrinogen alpha chain proteins


Figure 7. ZNF226 zf-C2H2 structural domains highlighted on the conceptual translation


Figure 8. ZNF226 zf-C2H2 structural domains highlighted on the conceptual translation


Figure 9. Sequence logo of ZNF226 zf-C2H2 structural domain DNA binding sites


AlphaFold prediction of ZNF821 Protein.


Divergence Rate of ZNF821 compared to Cytochrome c and Fibrinogen alpha.


A drawing of a prokaryotic cell


A diagram of an animal cell


The process of  cell division  in the animal  cell cycle


Active site, hydrophobic tunnel and lid-loop of acyl-protein thioesterases.


Mechanism of how acyl-protein thioesterases release their product by using a flexible lid-loop covering the substrate binding tunnel.   Nature Communications   8 (1):2201, Creative Commons Attribution 4.0 International License,  https://creativecommons.org/licenses/by/4.0/


Histology  features of a  lipoblast , also known as an adipocyte precursor cell or preadipocyte.


Differentiated Adipocyte stained with  Oil Red O


ADP-ribose


Mechanism for ADP-ribosylation, with residues of the catalyzing enzyme shown in blue. [ disputed  –  discuss ]


Crystal structure of PARP1 zinc finger domain bound to DNA (purple). PDB: 4AV1


DNA repair facilitated by PARP1 recruitment of repair enzymes. Repair of a single strand break in DNA is initiated by the binding of PARP1. PARP1 binds single-strand breaks and pulls base excision repair intermediates close, leading to the synthesis of poly(ADP-ribose). XRCC1 is the X-ray repair cross complementing protein 1. XRCC1 complexes with polynucleotide kinase (PNK) which processes DNA termini. PCNA is the proliferating cell nuclear antigen that serves as a DNA clamp that aids in the DNA polymerase activity (DNA pol) FEN1 (Flap endonuclease 1) is then recruited to remove the overhanging 5' flap. The last step of DNA repair involves DNA ligase which brings the final DNA strands together in a phosphodiester bond.


Crystal structure of the diphtheria toxin. PDB: 1MDT


He Jiankui


Steps of Alkaline lysis. Created in  https://BioRender.com


Enzymatic steps of alpha oxidation


Clockwise from top right:  Amoeba proteus ,  Actinophrys sol ,  Acanthamoeba  sp.,  Nuclearia thermophila .,  Euglypha acanthophora ,  neutrophil  ingesting bacteria.


The forms of  pseudopodia , from left: polypodial and lobose; monopodial and lobose; filose; conical; reticulose; tapering actinopods; non-tapering actinopods


Amoeba  phagocytosis  of a  bacterium


Foraminifera  have reticulose (net-like) pseudopods, and many species are visible with the naked eye.


Trophozoites  of the pathogenic  Entamoeba histolytica  with ingested  red blood cells


The first illustration of an amoeboid, from Rösel von Rosenhof's  Insecten-Belustigung  (1755)


Neutrophil  (white blood cell) engulfing anthrax bacteria


The  heterolobosean  pathogen  Naegleria fowleri  can behave as an amoeba (center) or as a flagellate (right).


The  choanoflagellate   Salpingoeca rosetta  can switch between a swimming ( flagellate ) stage and a crawling ( amoeboid ) stage when subjected to a confined space. [ 3 ]


Antimicrobial resistance.


Two stages in the constriction of apical surfaces (blue) of a pair of cells in  C. elegans .


Constriction of the apical side of cells in an epithelial layer generates enough force initiate invagination. In gastrulation, the apically constricting cells are known as bottle cells. The bottle shape results when constriction of the apical side of the cell squeezes the cytoplasm, thus expanding the basal side.


Apical constriction mechanisms (red: filamentous actin. orange: myosin.)


Apical constriction of cells at the hingepoints of  neural folds  generates forces that participate in  neural tube  closure.


Apoptotic DNA fragmentation, visualised by the  DNA laddering  assay (left). A  1 kb   marker  (middle) and  control  DNA (right) are included for comparison.


A  nucleosome , consisting of DNA (grey) wrapped around a  histone   tetramer  (coloured). In apoptotic DNA fragmentation, the DNA is cleaved in the  internucleosomal linker  region, which is the part of the DNA  not  wrapped around the histones.


Diagram of lipid vesicles showing a solution of biomolecules (green dots) trapped in the vesicle interior.


Standard artificial cell (top) and drug delivery artificial cell (bottom).


Representative types of artificial cell membranes.


Schematic representation of encapsulated cells within artificial membrane.


This diagram depicts the organization of a typical  mitotic spindle  found in  animal  cells.  Chromosomes are attached to kinetochore microtubules via a multiprotein complex called the  kinetochore .  Polar microtubules interdigitate at the spindle midzone and push the spindle poles apart via motor proteins.  Astral microtubules anchor the spindle poles to the cell membrane.  Microtubule polymerization is nucleated at the  microtubule organizing center .


The autophagic process is divided into five distinct stages: Initiation, phagophore nucleation, autophagosomal formation (elongation), autophagosome-lysosome fusion (autophagolysosome) and cargo degradation. [ 1 ]


A microscopic image of a prostate gland featuring an example of basal cells


A microscopic image of the human trachea, showcasing the typical location of basal cells (B) between the basement membrane (BM) and the remaining epithelium


TEM  image of the tracheal basal lamina in mice. The darkened areas with the arrows pointing to them display the location of hemidesmosomes connecting the layer of basal cells to the basal lamina.


A diagram displaying the layers of the epidermis, with basal cells comprising the stratum basale.


A diagram of cells in the respiratory epithelium. Basal cells are shown in purple, ciliated cells shown in brown, goblet cells are shown in green, and submucosal (below the epithelium) glands are shown in blue.


Diagram and histological examples showing the structure of gastric glands in different areas of the stomach. Note how the progenitor cells (which in this case is a term synonymous with basal cells) are located in the isthmus region of the pit in both examples, and how there is a single layer of cells that comprises the epithelium.


Diagram showing the location of intestinal crypts and the gradual migration of differentiating cells out of the crypt.


Reference ranges for blood tests  of white blood cells, comparing basophil amount (shown in violet) with other cells.


basophil activation and labeling


A diagrammatic illustration of the process of lipolysis (in a fat cell) induced by high  epinephrine  and low  insulin  levels in the blood. Epinephrine binds to a  beta-adrenergic  receptor in the cell wall of the adipocyte, which causes  cAMP  to be generated inside the cell. The cAMP activates a  protein kinase , which phosphorylates and activates a  hormone-sensitive lipase  in the fat cell. This lipase cleaves free fatty acids from their attachment to glycerol in the adipocyte. The free fatty acids and glycerol are then released into the blood.


A diagrammatic illustration of the transport of  free fatty acids  in the blood attached to  plasma albumin , its diffusion across the cell membrane using a protein transporter, and its activation, using  ATP , to form  acyl-CoA  in the  cytosol . The illustration is of a 12 carbon fatty acid.


A diagrammatic illustration of the transfer of an acyl-CoA molecule across the inner membrane of the  mitochondrion  by  carnitine-acyl-CoA transferase  (CAT). The illustrated acyl chain is 12 carbon atoms long. CAT is inhibited by high concentrations of  malonyl-CoA  (the first committed step in  fatty acid synthesis ) in the cytoplasm. This means that fatty acid synthesis and fatty acid catabolism cannot occur simultaneously in any given cell.


A diagrammatic illustration of the process of the  beta-oxidation  of an acyl-CoA molecule in the mitochondrial matrix. During this process an acyl-CoA molecule which is 2 carbons shorter than it was at the beginning of the process is formed. Acetyl-CoA, water and 5  ATP  molecules are the other products of each beta-oxidative event, until the entire acyl-CoA molecule has been reduced to a set of  acetyl-CoA  molecules.


General Mechanism of Beta Oxidation


Propionyl-CoA modification after beta oxidation of odd-chain fatty acid


Complete beta oxidation of  linoleic acid  (an unsaturated fatty acid).


Steps in beta-oxidation of odd-numbered saturated fatty acids [ 15 ]


Schematic demonstrating  mitochondrial   fatty acid   beta-oxidation  and effects of  long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency, LCHAD deficiency


A biconcave disc


The biocrystallization inhibitor  chloroquine  was developed in Germany in the 1930s. For 20 years Chloroquine was a "magic bullet".


Multiplex analysis of circulating tumor cells using QuantiGene ViewRNA CTC Platform


The grey represents the concentration of a molecule


Depicts migration of cells in response to types of molecules in the gradient.


Walter Sutton  (left) and  Theodor Boveri  (right) independently developed different parts of the chromosome theory of inheritance in 1902.


Diagram of the protein NJMU-R1's  secondary structure  and  post-translational modifications . [ 10 ]


Immunohistochemistry  staining of the mouse  cerebellum  for the protein NJMU-R1 in green. [ 11 ]


Human C17orf75 orthologs in select species obtained from a  BLASTP  search using the human protein with accession number:  NP_071739.2 .


Figure 1: An evoked calcium spark, in a cardiac muscle cell.


The  Lewis structure  of a  carbon  atom, showing its four  valence electrons


Schematic of  photosynthesis  in plants. The  carbohydrates  produced are stored in or used by the plant. Photosynthesis is  foundation  of  food  on Earth


F-actin  distribution in the cell cortex as shown by  rhodamine   phalloidin  staining of  HeLa  cells that constitutively express  Histone H2B - GFP  to mark  chromosomes .  F-actin  is thus red, while  Histone H2B  is displayed in green. The left-hand cell is in  mitosis , as demonstrated by  chromosome  condensation, while the right-hand cell is in  interphase  (as determined by intact  cell nucleus ) in a suspended state. In both cases,  F-actin  is enriched around the cell periphery. Scale bar: 10 micrometers.


A counting chamber


A picture of  Staphylococcus aureus  colonies growing on an  agar plate  (photographed in  transmitted light ). Such homogeneously spread colonies are suitable for CFU enumeration.


The electrode of a Coulter counter


A spectrophotometer


DAPI (magenta) bound to the minor groove of DNA (green and blue). From  PDB :  1D30 .


Laboratory cell disruptor


a    Cells of the same lineage fuse to form a cell with multiple nuclei, known as a syncytium. The fused cell can have an altered phenotype and new functions such as barrier formation.    b   Cells of different lineage fuse to form a cell with multiple nuclei, known as a heterokaryon. The fused cells might have undergone a reversion of phenotype or show transdifferentiation.    c   Cells of different lineage or the same lineage fuse to form a cell with a single nucleus, known as a synkaryon. New functions of the fused cell can include a reversion of phenotype, transdifferentiation and proliferation. If nuclear fusion occurs, the fused nucleus initially contains the complete chromosomal content of both fusion partners (4N), but ultimately chromosomes are lost and/or re-sorted (see arrows). If nuclear fusion does not occur, a heterokaryon (or syncytium) can become a synkaryon by shedding an entire nucleus.


BTX ECM 2001 Electrofusion generator cell fusion applications manufactured by BTX Harvard Apparatus, Holliston MA USA


General stages of cell lineage (cell lineage of liver development in red)


Typical prokaryotic cell structure


Typical eukaryotic animal cell structure


Ion Transport: Direction of Na/K flow


Endocytosis in Animal Cells


Polarized localization of  Staufen protein  (white arrow) in  Drosophila  stage 9 oocyte (Stau:GFP, DAPI).


Pluripotent , embryonic  stem cells  originate as inner mass cells within a  blastocyst . These stem cells can become any tissue in the body, excluding a  placenta . Only the  morula 's cells are  totipotent , able to become all tissues and a placenta.


A: Human  embryonic  stem cells (cell colonies that are not yet differentiated). B:  Nerve  cells


Naive human pluripotent stem cell colony here seen growing on feeder cells (mouse).


Ranunculus asiaticus  example of totipotency of two individuals  MHNT


Hematopoietic stem cells are an example of multipotency. When they differentiate into myeloid or lymphoid progenitor cells, they lose potency and become oligopotent cells with the ability to give rise to all cells of its lineage.


Human  cancer cells  with nuclei (specifically the DNA) stained blue. The central and rightmost cell are in  interphase , so the entire nuclei are labeled. The cell on the left is going through  mitosis  and its DNA has condensed.


Drawing of the structure of  cork  by  Robert Hooke  that appeared in  Micrographia


Matthias Jakob Schleiden  (1804–1881)


Theodor Schwann  (1810–1882)


Adoptive T-cell therapy. Cancer specific T-cells can be obtained by fragmentation and isolation of tumour infiltrating lymphocytes, or by genetically engineering cells from peripheral blood. The cells are activated and grown prior to transfusion into the recipient (tumour bearer).


Charles-Édouard Brown-Séquard  – tried to stop aging by injecting animal testicle extract.


The most common processes of cell unroofing. (left) Sandwich of two cells between two coverslips. (right) Lateral flux of medium allows to break the cells.


Example of translocation of cargo through direct penetration


Types Endocytosis Mediated by Cell-Penetrating Peptides


Translocation Mediated by the Formation of Inverted Micelles


Translocation Mediated by a Transitory Structure


Covalent linkage between CPP and nucleic acid


An improved substrate for CPP that minimize the proteolysis effects


Folding control of CPP using unnatural β, δ cyclic amino acids


Quantum dots applications as cell labeling


Examples of metal chelates successfully delivered into cells


Illustration of adipocytes of different sizes. In response to dietary excess energy intake, adipocytes adapt by increased storage of lipids, resulting in cellular hypertrophy.


Figure 1.  Snapshot images taken from a video showing the nucleation and growth of a TEM in an endothelial cell intoxicated with C3 exoenzyme from  Clostridium botulinum  for 24 hours, Bar = 10 μm. For the dynamics see  Video .


Figure 2.  Analogy between  liquid dewetting  and cellular dewetting.


PcG proteins repress transcription in salivary glands. A shows an active transcription. B shows transcription after addition of a promoter. C shows transcription of a mutant protein. D shows transcription become depressed.


Salmonella  bacteria (red) invade cultured human cells


A schematic illustration of a dual reporter study. Each data point corresponds to a measurement of the expression level of two identically regulated genes in a single cell: the scatter reflects measurements of a population of cells. Extrinsic noise is characterised by expression levels of both genes covarying between cells, intrinsic by internal differences.


A canonical model for stochastic gene expression, known as the two-state or telegraph  [ 30 ]  model. DNA flips between "inactive" and "active" states (involving, for example,  chromatin remodelling  and  transcription factor  binding). Active DNA is transcribed to produce mRNA which is translated to produce protein, both of which are degraded. All processes are  Poissonian  with given rates.


Schematic of chemically induced dimerization.  Two proteins that do not normally interact (top) bind in the presence of a dimerizing agent (bottom).


An ion gradient has  potential energy  and can be used to power  chemical reactions  when the ions pass through a  channel  (red).


Oxidative phosphorylation  involves two processes — the  electron transport chain  and chemiosmosis — and occurs in  mitochondria .


Energy conversion by the inner mitochondrial membrane and chemiosmotic coupling between the  chemical energy  of redox reactions in the  respiratory chain  and the  oxidative phosphorylation   catalysed  by the  ATP synthase . [ 6 ] [ 7 ]


A diagram of chemiosmotic phosphorylation


Directions of chemiosmotic proton transfer in the  mitochondrion ,  chloroplast  and in  gram-negative bacterial  cells ( cellular respiration  and  photosynthesis ). The bacterial  cell wall  is omitted,  gram-positive bacterial  cells do not have outer membrane. [ 6 ]


Chemiosmotic coupling between the energy of sunlight,  bacteriorhodopsin  and phosphorylation ( chemical energy ) during  photosynthesis  in the  halophilic  archaeal organism  Halobacterium salinarum  (syn.  H. halobium ). The archaeal  cell wall  is omitted.  [ 6 ] [ 7 ]


Early cell powered by external proton gradient near a deep-sea hydrothermal vent. As long as the membrane (or passive ion channels within it) is permeable to protons, the mechanism can function without ion pumps. [ 10 ]


Typical structure of a  chemokine receptor , with seven transmembrane helices and a characteristic "DRY" motif in the second intracellular loop.  Chemokine receptors are usually linked to a  G-protein  through which they signal.


Chemokinesis


Chemotactic drug-targeting


Chemotactic selection


Chief cells are part of  fundic gland polyps  (here shown in high magnification). [ 11 ]


In the diagram, (1) refers to a chromatid: 1-half of two identical threadlike strands of a replicated  chromosome . During cell division, the identical copies (called a " sister chromatid pair ") are joined at the region called the  centromere  (2). Once the paired sister chromatids have separated from one another (in the  anaphase  of   mitosis ) each is known as a daughter chromosome. The short arm of the right chromatid (3), and the long arm of the right chromatid (4), are also marked.


Schematic  karyogram  of the human chromosomes, showing their usual state in the G 0  and G 1  phase of the cell cycle. At top center it also shows the chromosome 3 pair in  metaphase  (annotated as "Meta."), which takes place after having undergone  DNA synthesis  which occurs in the  S phase  (annotated as S) of the cell cycle. During metaphase, each chromosome is duplicated into  sister chromatids . Further information:  Karyotype


Condensation and resolution of human sister chromatids in early mitosis


A . "Budding"  nucleus  with nucleoplasmic bridge (arrow), a chromatin bridge after mitosis.


A.   Microtubules  localized at a chromatin bridge. These polymers are stained with anti-tubulin antibody and viewed using  fluorescence microscopy .  B.  Merged images of two daughter cells connected by a chromatin bridge. The fluorescence techniques of  indirect immunofluorescence  and DAPI staining were utilized.  C.  The same cells visualized using DAPI staining.


A  chromatin  bridge, visualized using DAPI staining.


Immunodetection of a  chromosome  showing  DNA  (blue) and two scaffold proteins:  SMC2  (red) and  topoisomerase IIα  (green) [ 1 ]


EVOS Imaging depicting a single celled organism with distinctive cilia


Cilia Structure


Mechanism for Citrate Synthase (including residues involved)


In this  electron micrograph  of a cell, the cleavage furrow has nearly completely divided the cell.


Cilliate undergoing the last processes of binary fission, with the cleavage furrow being clearly visible.


Clonal expansion  and monoclonal versus polyclonal proliferation


Electron micrograph of in vitro–formed COPI-coated vesicles. Average vesicle diameter at the membrane level is 60 nm.


The COPI triad. Color scheme: membrane - gray; Arf1 - pink; gamma-COP - light green; beta-COP, dark green; zeta-COP - yellow; delta-COP - orange; betaprime-COP - light blue; alpha-COP - dark blue


Human Sar1A bound to GDP


Titan Krios at the  University of Leeds


Single particle analysis  workflow


This schematic shows the concept of electron tomography. A sample is imaged in a TEM as it is tilted to different angles, resulting in a "tilt-series" of 2D images (top). This tilt-series is then computationally reconstructed into a 3D "tomogram" (bottom).


Central slice through a tomogram of an intact  Bdellovibrio bacteriovorus  cell. Scale bar 200 nm.


(a)  Tomographic slice of a cardiac sarcomere. Scale bar, 50 nm.  (b)  Reconstructed filaments mapped into a tomogram. Scale bar, 50 nm  (c)  Structure of the thick filament from the M-band to the C-zone. [ 10 ]


Schematic showing information transfer for various tilt schemes. Tilts are shown from −60° to +60° in 3° increments for 41 total tilts. Grey values correspond to the information transfer at each tilt according to the color map shown on the left. Reduction in information transfer is attributed to higher tilts having increased apparent thickness of the sample and accumulated radiation damage throughout the collection scheme. [ 18 ]


The human cerebral cortex divided into  Brodmann areas  on the basis of cytoarchitecture.


Transmission   electron micrograph  of a  chondrocyte , stained for calcium, showing its nucleus (N) and mitochondria (M).


Cytometers  are the instruments which count the blood cells in the common blood test.


A  hemocytometer


Model A  Coulter Counter  — The first commercial flow cytometer


Cells shown with  immunostaining  observed with a  confocal microscope .


Cytonemes take up and transport morphogens. This micrograph shows tissues from a  Drosophila  larva whose tracheal cells are marked with membrane-tethered mCherry fluorescent protein. Some of the cytonemes that extend from the tracheal branch contact the underlying wing imaginal disc and transport the Dpp morphogen protein (marked with green fluorescent protein) to the tracheal cells. [ citation needed ]


Structure of a death domain protein.  1ngr


A  decellularized aortic homograft


Principle of  tissue engineering


The degranulation process in a Mast cell. 1 =  antigen ; 2 =  IgE ; 3 =  FcεR1 ; 4 = preformed mediators ( histamine ,  proteases ,  chemokines ,  heparin ); 5 = granules; 6 - Mast cell; 7 - newly formed mediators ( prostaglandins ,  leukotrienes ,  thromboxanes ,  platelet-activating factor )


Crystallographic structure of  human phosphatase and tensin homolog  (PTEN). The  active site  of the blue  N-terminal  phosphatase domain is shown in yellow. The  C-terminal  C2 domain is shown in red. [ 7 ]


The ancestral state reconstruction and cross-species orthologous alignment. a Ancestral state reconstruction for human Val129 (red arrow) based on the Maximum Parsimony (MP) method in MEGA11. b Regional alignment comprising the human Val129 site (black arrow above the alignment).


Differential centrifugation


DNA laddering (left) visualised in an  agarose gel  by  ethidium bromide  staining. A  1 kb   marker  (middle) and  control  DNA (right) are included.


Overview of normal chromosome duplication in the cell cycle


S. cerevisiae  origin in the prereplicative state. Assembly of the pre-replicative complex (pre-RC) readies the origin for firing.


S. cerevisiae  origin in the postreplicative state. CDK-mediated phosphorylation of the pre-RC components prevents origins from re-licensing.


This is a graph showing the effect of fractionation on the ability of  gamma rays  to cause cell death. The blue line is for cells which were not given a chance to recover; the red line is for cells which were allowed to stand for a time and recover.


The Dounce homogenizers, devices used for mechanical lysis of tissue or cells, were invented by and named after Alexander Dounce.


Homogenized mouse hippocampus at the bottom of a Dounce homogenizer tube.


Cells release eat-signals onto their surface to induce phagocytes to eat them


Crystal structure of  Thermotoga maritima   encapsulin . PDB entry  3dkt


Endocycling vs. endomitosis


Notch regulation of endocycling


Phospholipids, cholesterol (orange spheres) and two apolipoprotein A-1 chains (pink ribbon) interaction


Triglyceride Structure


Lipid Metabolism


The triggers and consequences of entosis in cancer [ 7 ]


Blood cell lineage


Histology of an eosinophil within  epithelium , characterized by its bilobed nucleus despite scant visible eosinophilic cytoplasm.


Reference ranges for blood tests  of white blood cells, comparing eosinophil granulocyte amount (shown in light red) with other cells


Apocrine  cells, showing  apical snouts  towards the lumen.


Structure of 19,20-epoxydocosapentaenoic acid, an example of an epoxydocosapentaenoic acid. Both the 19( R ),20( S )- and 19( S ),20( R )-EDP are produced by epoxygenases.


Chemical structure of 14,15-epoxyeicosatrienoic acid


A mature  gastrotrich , with visible cells on the surface. Further growth will now occur solely by cell enlargement.


The distribution of the  total body water  in  mammals  between the  intracellular compartment  and the extracellular compartment, which is, in turn, subdivided into  interstitial  fluid and smaller components, such as the  blood plasma , the  cerebrospinal fluid  and  lymph


Cell membrane details between extracellular and intracellular fluid


Sodium–potassium pump and the diffusion between extracellular fluid and intracellular fluid


Differences in the concentrations of ions giving the membrane potential


Formation of interstitial fluid from blood


Diagram showing the formation of lymph from interstitial fluid (labeled here as "tissue fluid"). The tissue fluid is entering the blind ends of  lymph capillaries  (shown as deep green arrows).


"Flagellata" from  Ernst Haeckel 's  Artforms of Nature , 1904


Parasitic  Excavata  ( Giardia lamblia )


Green algae  ( Chlamydomonas )


"Flagellata" from  Encyclopædia Britannica


Schematic diagram of a flow cytometer, from sheath focusing to data acquisition.


Analysis of a marine sample of  photosynthetic   picoplankton  by flow cytometry showing three different populations ( Prochlorococcus ,  Synechococcus , and  picoeukaryotes )


Flow cytometry gating into main categories of  blood cells  by  side scatter  and  CD45 , in a case with normal distributions.


Cell Sorting Using Flow Cytometry and Droplet Technology


Use of flow cytometry to measure copy number variation of a specific DNA sequence ( Flow-FISH )


Flow cytometry using  7-Aminoactinomycin D  (7-AAD), wherein a lower signal indicates viable cells. Therefore, this case shows good viability.


Claude Bernard, French physician who introduced the concept of homeostasis


Schematic diagram of fluorochromasia molecular mechanism


Histopathologic image of  aspiration pneumonia  in an elderly patient with debilitating neurologic illness. Note foreign-body giant cell reaction. Autopsy case. H & E stain.


Cut that creates a sticky end


Cut that creates a blunt end


Fragmentation is the third and final step of cell disassembly during apoptosis (right side of scheme). [ 9 ]


A blood smear from a patient with hemolytic anemia, showing schistocytes


Natural freeze-fracture. An iceberg fractured off a glacier. Erosion reveals the layering hidden within the original glacier


Snowflake macro photography


Two forms of amorphous ice. High density (HDA) top and low density amorphous (LDA) ice bottom


Iceplanet


Freeze-fracture and replicated yeast cell at -50°C with two prominent circular bud scars. The ice surrounding the cell melted due to the heat of the fracture, flowed a few microns, and quickly refroze again.


Ice blocks are cut and loaded onto a horse drawn sled circa 1935


Ais kacang


Fracture failure of a steel pipe due to cold temperatures


Concrete fracture


Platinum coated surface of fracture face of glass reinforced plastic SEM Stereo 500x


Freeze-fracture Replication shielding block built in 1984 after Bullivant and Ames 1966


Commercial Freeze Etching Replication device circa 2000


The interior of a sheep lens cell plasma membrane. The smooth areas mainly at the top of the picture are mainly lipid membrane. The rough areas correlate to areas of protein in the membrane. When viewed closely the Freeze-fracture replica immunolabling (FRIL) reveals the gold beads averaging 5nm in size coated in anti-Cxn46 antibodies. They pepper the visible portion of the gap junction containing the protein [ 17 ]


Drosophila   ovariole : spectrosomes are the red round structures in germline stem cells. The red branched structures in 2-cell and 8-cell cysts are the fusomes.


A wild type  D. melanogaster  testis showing the fusome (spectrin, green), DNA (DAPI, blue), and germ cells (vasa, red). The fusome connects cells in a cyst and becomes branched as the cyst grows with cell divisions. Image by S. Brantley, used with permission by the author.


GemIdent logo


GemIdent identifying oranges in an orange grove


GemIdent identifying cancer cells in a microscopic image


GemIdent identifying cancer cells, T-cells, and background nuclei in a microscopic image


GemIdent analyzing results using data analysis and visualization tools


Old World  distribution of hemoglobin-inherited disorders


This vein (4) shows the interaction between the malaria sporozoites (6) with sickle cells (3) and regular cells (1). While malaria is still affecting the regular cells (2), the ratio of sickle to regular cells is 50/50 due to sickle cell anemia being a heterozygous trait, so the malaria cannot affect enough cells with schizonts (5) to harm the body.


Hemolytic anemia due to G6PD deficiency following Fava beans consumption


stained red blood cell membrane proteins on electrophoresis gel strip [ 46 ]


Red Blood Cell membrane major proteins


Old World distribution of enzymopathies and immunogenetic variants


Survival curves of  Luo  children in an area of Kenya where malaria transmission is intense. HbAS: Heterozygous sickle-cell hemoglobin; HbAA: normal hemoglobin; HbSS: homozygous sickle-cell hemoglobin.  [ 67 ]


Flowchart for GESTALT workflow.


Diagram describing the transgenic zebrafish engineered for scGESTALT.


Multinucleated giant cells due to an infection.  H&E stain .


CD68   immunostaining  demonstrating giant cells and macrophages


Foreign-body giant cells in the lung. H&E stain.


Foreign-body giant cell reaction to a suture. H&E stain.


Glycosomes in the trypanosomatid


By taking advantage of the pores in the membrane of the glycosome, a drug can enter the organelle and be used to kill the trypanosoma brucei


Crystallographic structure  of the human  κ-opioid receptor  homo  dimer  ( 4djh ) imbedded in a cartoon representation of a  lipid bilayer .  Each protomer is individually rainbow colored ( N-terminus  = blue,  C-terminus  = red).  The receptor is complexed with the  ligand   JDTic  that is depicted as a  space-filling model  (carbon = white, oxygen = red, nitrogen = blue). [ 1 ]


Most common molecular motif of hemicellulose


Section of a cell wall; hemicellulose in green


Xylan in hardwood [ 8 ]


Beta-D-glucopyranose with carbon positions.


A Petri dish with  bacterial  colonies on an  agar -based  growth medium


Hemicellulose contribution to structural support within plant cells


Heterokaryon in fungal mitosis


Sketch of cork through a microscope. Cork was one of the first substances examined by  Robert Hooke  through his microscope and he found that it was composed of thousands of minute pockets he named "cells".


A micrograph from a Transmission Electron Micrograph showing a lipid vesicle. The two dark bands are the two leaflets comprising the bilayer. Similar images taken in the 1950s and 1960s confirmed the bilayer nature of the cell membrane


Diagram of a cell membrane showing integral and peripheral membrane proteins


Fruit body of a slime mold, possibly  Tubifera ferruginosa . The clearly visible white material is the hypothallus.


Histological slide of the human herpes virus-6 showing infected cells, with inclusion bodies in both the nucleus and the cytoplasm.


CT scan in a patient with chronic lymphocytic leukemia, showing splenomegaly. Yellow arrows point at the spleen.


A bag with bone marrow stem cells ready to be used for transplant


necrosis


Interior of a  CO 2  incubator used in  cell culture


A Bacteriological incubator


Reaumur thermometer


Incubator invented by Hess


Shaking incubator


Some induced cell cycle arrests are done in Xenopus (frog) oocytes


Phases of the cell cycle


Mitosis is the non-interphase part of the  cell cycle  and generates two daughter cells


Bcl-2 Crystal Structure with visible domains


Poliovirus  genome, including an IRES.


An illustration of interphase. The  chromatin  has not yet condensed, and the cell is undergoing its normal functions.


An image of the nucleus of a cell ( HT1080 ) currently in interphase (likely G1).  Note:   Cytoplasm  of this cell or the neighboring cell is not visible (top-left), which is currently in the  telophase  of  mitosis . Image taken using an optical microscope and  DAPI  staining of DNA.


Process of how macroautophagy works


Functions of autophagy


pH gradient across a membrane, with protons traveling through a transporter embedded in the membrane.


Approximate pHs of various organelles within a cell. [ 6 ]


Protons being pumped from the mitochondrial matrix into the intermembrane space as the electron transport chain runs, lowering the pH of the intermembrane space.


Karyogamy in the context of cell fusion. 1-haploid cells, 2-cell fusion, 3-single cell with two pronuclei, 4-fusing pronuclei (karyogamy), 5-diploid cell


Step labeled number 4 indicates karyogamy's place in the context of the life cycle of the fungus  Taphrina .


(a) In fission yeast, the mating process is triggered by nitrogen starvation when compatible partners are present. (b) Budding yeast cells of opposite mating type can instead mate spontaneously on rich medium to form stable diploids that undergo sporulation upon starvation. In both organisms after pheromone exchange, cells grow in a polarized manner in the direction of their partner and undergo fusion, karyogamy and sporulation.


Nucleus is gray; Spindle pole body (SPB) is black circle; Microtubules (MTs) are black bars; actin filaments are gray cables; actin patches are small gray circles. (A) Nuclear orientation to the shmoo tip. (B) MT attachment to the shmoo tip. (C) Before cell–cell fusion, MTs are maintained at the shmoo tip. (D) Sliding cross-bridge model for nuclear congression. Oppositely oriented MTs overlap and are cross-linked along their lengths, whereas depolymerization is induced at the spindle poles. (E) Plus end model for nuclear congression. MT plus ends cross-link and induce depolymerization to draw opposing nuclei together.


(Left Side) A karyosome with a capsule. (Right Side) A karyosome without a capsule.


Micrographic  karyogram of human male using  Giemsa  staining


Schematic  karyogram demonstrating the basic knowledge needed to read a karyotype


Chromosomes at various stages of  mitosis . Karyograms are generally made by chromosomes in prometaphase or metaphase. During these phases, the two copies of each chromosome (connected at the  centromere ) will look as one unless the image resolution is high enough to distinguish the two.


Micrograph of human chromosomes before further processing. Staining with Giemsa confers a purple color to chromosomes, but micrographs are often converted to  grayscale  to facilitate data presentation and make comparisons of results from different laboratories. [ 7 ]


Micrographic karyogram of a human male. See section text for details.


Schematic karyogram of a human. Even at low magnification, it gives an overview of the  human genome , with numbered chromosome pairs, its main changes during the  cell cycle  (top center), and the  mitochondrial genome  to scale (at bottom left). See section text for more details.


The  cell cycle


Karyogram from a human female  lymphocyte  probed for the  Alu sequence  using  FISH


Spectral karyogram of a human female


Spectral human karyotype


Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere


Image of kinetochores in pink


Kinetochore structure and components in vertebrate cells. Based on Maiato  et al.  (2004). [ 9 ]


Fluorescence microscopy micrographs, showing the endogenous human protein  Mad1  (one of the spindle checkpoint components) in green, along the different phases in mitosis;  CENP-B , in red, is a centromeric marker, and  DAPI  (in blue) stains DNA


Chromosomes attach to the  mitotic spindle  through sister kinetochores, in a bipolar orientation


Scheme showing cell cycle progression between prometaphase and anaphase. (Chromosomes are in blue and kinetochores in light yellow).


Metaphase cells with low CENP-E levels by  RNAi , showing  chromosomes unaligned at the metaphase plate (arrows). These chromosomes are labeled with  antibodies  against the mitotic checkpoint proteins Mad1/Mad2. Hec1 and CENP-B label the centromeric region (the kinetochore), and DAPI is a specific stain for DNA.


Scheme showing different anchoring configurations between chromosomes and the mitotic spindle. [ 55 ]


Transmission electron micrograph  of L-form  Bacillus subtilis . The cells lack the electron-dense  cell wall  of normal  bacteria . Scale bar is 500  nanometers .


Transmission electron micrograph of a population of L-form  Bacillus subtilis , showing a range of sizes. Scale bar is 10  micrometers .


Phase contrast image of L-form cells from  Bacillus subtilis  showing a range of sizes. Scale bar is 5 micrometers.


Granulation tissue with a poorly formed granuloma to the left of centre. Within this area there is a multinucleate giant cell of the Langhans type. The patient had a healing mycobacterial infection of the skin ( Mycobacterium ulcerans  infection).


Lipoblast features.


Structure of the lipoteichoic acid polymer


Gram-positive and -negative cell walls


Plasmolysis


Sodium dodecyl sulfate (SDS) structure


Triton X-100 structure


Drawing of a macrophage when fixed and stained by  giemsa dye


Steps of a macrophage ingesting a pathogen:   a.  Ingestion through phagocytosis, a phagosome is formed b.  The fusion of lysosomes with the phagosome creates a  phagolysosome ; the pathogen is broken down by enzymes  c.  Waste material is expelled or  assimilated  (the latter not pictured)  Parts: 1.   Pathogens 2.   Phagosome 3.   Lysosomes 4.  Waste material 5.   Cytoplasm 6.   Cell membrane


Gram stain  of a macrophage with ingested  S. epidermidis  bacteria, seen as purple granules within its  cytoplasm .


A macrophage stretching its "arms" ( filopodia ) [ 39 ]  to engulf two particles, possibly pathogens, in a mouse ( trypan blue exclusion  staining).


Melanophage. H&E stain.


CyTOF mass cytometer.


Illustration depicting mast cell activation and anaphylaxis


Mast cell


The role of mast cells in the development of allergy.


Structure of histamine


Structure of FcεR1 on mast cell. FcεR1 is a tetramer made of one alpha (α) chain, one beta (β) chain, and two gamma (γ) chains. IgE is binding to α chain, signal is transduced by ITAM motifs on β and γ chains.


The image shows a membrane-bound ribosome synthesizing a protein into the lumen of the endoplasmic reticulum. Image by wiki user Christinelmiller.


The image shows the translocation of a ribosome and the role of the SRP. Image by wiki user Czwieb.


Mesangial cells (colored in purple) as seen within intraglomerular and extraglomerular mesangium.


Methanobactin OB3b. PDB  2xji [ 2 ]


Microbody structure - a peroxisome


Microdialysis probes manufactured by CMA Microdialysis AB, Kista, Sweden


Schematic illustration of a  microdialysis probe


Actin cytoskeleton of  mouse   embryo   fibroblasts , stained with  Fluorescein isothiocyanate - phalloidin


Plate 4, Figure 9 from the book, showing drawings of what are now  called  Schwann cells  in the  vagus nerve  of a  calf .


Transmission electron micrograph of lead citrate stained microvesicles. Black bar is 100 nanometers


The process of the formation of exosomes. 1. Cell undergoes endocytosis forming endocytic vesicles. 2. Endocytic vesicles fuse together forming an early endosome. 3. Endocytic cisterna matures into exocytic multivesicular body, during which membrane invaginations form exosomes. 4.Multivesicular body fuses with the plasma membrane, releasing exosomes into the extracellular space.


A middle stage midbody stained with tubulin


Structure of Milk fat globule membrane in the mammary alveolus


Mitochondrial proteins encoded from the nuclear genome need to be targeted and transported appropriately into the mitochondria.


The processes of fusion and fission allow for mitochondrial reorganization.


Cell shape changes as a function of  mitotic phase . Shown is an example of a  HeLa cell  cultured on a glass surface. For visualization of  DNA  and  mitotic phase  assignment, the cell expresses  Histone H2B - GFP  to provide  fluorescent  labeling of  chromosomes . Transmitted light ( DIC ),  fluorescence  ( GFP ), and merged images are shown every 4 minutes as the cell transitions from  G2 phase  through  mitosis  to  telophase / G1 phase .


Angle description in DNA structure


Diagrammatic representation of Watson and Crick's DNA structure


Griffith's experiment


Hershey–Chase experiment


Meselson-Stahl experiment


Schematic relationship between  biochemistry ,  genetics  and molecular biology


DNA animation


Transduction image


Two percent  agarose gel  in  borate buffer cast  in a gel tray


SDS-PAGE


Proteins stained on a PAGE gel using Coomassie blue dye


Northern blot diagram


Hybridization of target to probe


Fig.1 Schematic figure of Maxwell's demon thought experiment. The demon distinguishes fast-moving molecules from slow-moving ones and opens the small hatch selectively to let the fast-moving molecules pass from a A to B and the slow-moving molecules from B to A. Compartment B heats up whereas A cools down with respect to the average temperature although no work is done. It seems there is a contradiction with the second law of thermodynamics. But the ability to distinguish requires the gain of information, which is a form of energy; therefore. the system obeys the second law of thermodynamics inasmuch as information is first gained but then erased.


Fig.2 The protein demon (blue) and the substrate or ligand (orange) go through a cycle in which the electromagnetic interaction (1' --> 2) between the two, following the induced fit, causes a conformational change upon which the substrate is released (2'). Hydrolysis of ATP brings the protein back to its original state


Comparison of monoblast, promonocyte and monocyte.


Artist's impression of monocyte


A  scanning electron microscope  (SEM) image of normal circulating human blood. One can see red blood cells, several knobby white blood cells including lymphocytes, a monocyte, a neutrophil, and many small disc-shaped platelets.


Reference ranges for blood tests  of white blood cells, comparing monocyte amount (shown in green) with other cells.


Tulip flower showing mosaicism


Myoepithelioma , here with  plasma cell -like myoepithelial cell.


Haptotaxis


Figure 2. Mechanisms of neural development dependent of neuronal self-recognition. Self-avoidance ensures that there is no overlap of isoneural branches and is at the basis of neuronal circuit assembly.


Figure 3. Nervous system of the medicinal leech ( H. medicilanis )


Figure 4. Subfields of leech mechanosensory axons compete for territory. Wild type leech mechanosensory neuron with three separate subfields innervating adjacent regions of the epidermis (A). If the growth cone of one branch is crushed (B) or delayed (C), the sibling subfields grow occupying the free territory. Simplified diagrams, based on results in Kramer & Stent, 1985)


Figure 6. Timeline regarding important discoveries about neuronal self-avoidance. Authors and organisms utilized in the studies are presented.


A scanning electron microscope image of NETs engulfing fungal cells ( Candida albicans ) in an infected mouse lung. (Click on image for more details.) [ 1 ]


Fluorescent image of cultivated neutrophils isolated from venous blood of human with Alzheimer Disease. Sample was treated with Hoechst 33342 dye that is used to stain DNA. The picture shows the release of DNA by a neutrophil as foggy area in the center of the view field indicating the spontaneous activation of neutrophil extracellular traps (NETs) formation in AD patients that is not usually observed in healthy mates. Magnification x40.


Neutrophil granulocyte migrates from the blood vessel to the matrix, secreting proteolytic enzymes to dissolve intercellular connections (to the improvement of its mobility) and envelop bacteria through phagocytosis.


Hypersegmented neutrophil


Reference ranges for blood tests  of white blood cells, comparing neutrophil amount (shown in pink) with that of other cells


HSC= hematopoietic stem cell , Progenitor= progenitor cell , L-blast= lymphoblast ,  lymphocyte , Mo-blast= monoblast ,  monocyte ,  myeloblast , Pro-M= promyelocyte ,  myelocyte , Meta-M= metamyelocyte , neutrophil,  eosinophil , basophil, Pro-E=proerythroblast, Baso-E=basophilic erythroblast, poly-e= polychromatic  erythroblast, ortho-E=orthochromatic erythroblast,  erythrocyte ,  promegakaryocyte ,  megakaryocyte ,  platelet


Scanning electron micrograph  of a neutrophil (yellow) phagocytosing  anthrax bacilli  (orange). Scale bar is 5 μm.


Micrograph showing several neutrophils during an acute inflammation


Activity of neutrophil-killer and neutrophil-cager in NBT test [ 71 ]


Figure 1: This figure shows neutrophil swarming starts and stops. [ 12 ]


Non-mevalonate pathway reactions in the biosynthesis of isoprenoids.  Redrawn verbatim from the scheme of Qidwai and coworkers [Fig. 2.]. [ 9 ]  Note, the enzyme abbreviations in this figure are non-standard (cf. Eisenreich et al. [ 10 ] ), but are presented here and reproduced in the table to allow the two sets of data to be used together.


Confocal microscopic  analysis of  dermal fibroblasts  in primary culture from a control (a and b) and the subject with  progeria  (c and d). Labelling was performed with anti- lamin  A/C antibodies. Irregularly shaped  nuclear envelopes  are seen in many of the progeria  fibroblasts .


Structure and function of the nuclear lamina. The nuclear lamina lies on the inner surface of the inner nuclear membrane (INM), where it serves to maintain nuclear stability, organize chromatin and bind nuclear pore complexes (NPCs) and a steadily growing list of nuclear envelope proteins (purple) and transcription factors (pink). Nuclear envelope proteins that are bound to the lamina include nesprin, emerin, lamina-associated proteins 1 and 2 (LAP1 and LAP2), the lamin B receptor (LBR) and MAN1. Transcription factors that bind to the lamina include the retinoblastoma transcriptional regulator (RB), germ cell-less (GCL), sterol response element binding protein (SREBP1), FOS and MOK2. Barrier to autointegration factor (BAF) is a chromatin-associated protein that also binds to the nuclear lamina and several of the aforementioned nuclear envelope proteins. Heterochromatin protein 1 (HP1) binds both chromatin and the LBR. ONM, outer nuclear membrane. [ 2 ]


BTX ECM 2001 Electrofusion generator used for nuclear transfer applications


Macromolecules , such as  RNA  and  proteins , are  actively transported  across the nuclear membrane in a process called the  Ran - GTP  nuclear transport cycle.


Figure 1: Schematic illustration of a linear OFM probe. Exchange of compounds between the open exchange area of the OFM probe and the surrounding interstitial fluid.


Figure 2: Schematic illustration of a concentric OFM probe.


Figure 3: OFM system for clinical use, up to 48 hours, consisting of catheter, tubing, perfusate bag, pump and sample collection, All products are CE-certified.


Figure 4: Linear aOFM/dOFM probe


Figure 5: Concentric cOFM probe consisting of sampling insert, guide, healing dummy, and lock (from left to right)


Overview of the main parts of an optical typical stretcher setup


Refraction of rays at the particle surface. For a particle centered on the beam axis, momentum transfer is in the direction of propagation (scattering force, up). A particle off the axis is pulled into the beam (gradient force, down).


The surface forces pull on the object mainly along the direction of propagation, leading to a deformation for sufficiently soft objects.


A photograph of a nanoparticle (diameter 103 nm) trapped by an optical tweezer. The nanoparticle can be seen as the tiny bright spot in the middle. For additional control two copper electrodes are placed above and below the particle.


Dielectric objects are attracted to the center of the beam, slightly above the beam waist, as described in the text. The force applied on the object depends linearly on its displacement from the trap center just as with a simple spring system. It is a restoring force and thus equal to

 −

 k

 t
 r
 a
 p

 x

 {\displaystyle -k_{\mathrm {trap} }x}

 .


Ray optics explanation (unfocused laser).  When the bead is displaced from the beam center (right image), the larger momentum change of the more intense rays cause a net force to be applied back toward the center of the laser. When the bead is laterally centered on the beam (left image), the resulting lateral force is zero. But an unfocused laser still causes a force pointing away from the laser.


Ray optics explanation (focused laser).  In addition to keeping the bead in the center of the laser, a focused laser also keeps the bead in a fixed axial position: The momentum change of the focused rays causes a force towards the laser focus, both when the bead is in front (left image) or behind (right image) the laser focus. So, the bead will stay slightly behind the focus, where this force compensates the scattering force.


A generic optical tweezer diagram with only the most basic components.


The Optical Cell Rotator is a fiber based laser trap that can hold and precisely orient living cells for tomographic microscopy.


Tonicity concept related to the transport of water towards the more concentrated  aqueous solution  ( osmotic transport ): In  isotonic  solutions, water flows equally into and out of the cell ( equilibrium ). In hypertonic solutions water flows out of the cell and the cell shrinks ( plasmolysis ). In hypotonic solutions, water flows into the cell and the cell swells ( turgescence ).


Light  micrograph  of a moss's leaf cells at 400X  magnification


An illustration of the stages of  mitosis  in a human cell from  Gray's Anatomy


Regulation of oxidation response in bacteria involving OxyR and SoxRS regulons


Mechanism of prevention of oxidative damage by enzymatic antioxidants


Oxidative stress mechanisms in tissue injury. Free radical toxicity induced by  xenobiotics  and the subsequent detoxification by cellular enzymes (termination).


Schematic of actin comet tail formation by  Listeria  using  ActA . The nucleation complex  Arp2/3  is recruited to ActA, a WASP mimic. Actin filament polymerization then takes place at the posterior end of the bacterium, propelling it through the host cell cytoplasm in the anterior direction.


Stages in the intracellular life-cycle of  Listeria monocytogenes . (Center) Cartoon depicting entry, escape from a vacuole, actin nucleation, actin-based motility, and cell-to-cell spread. (Outside) Representative electron micrographs from which the cartoon was derived.


Cartoon of paracytophagy during  Listeria  infection, progressing to secondary vacuole formation and escape.


Phagocytosis of a bacterium, showing the formation of phagosome and phagolysosome


Phagocytosis -- amoeba


Phosphorylation and dephosphorylation summary


Structure of the photoactivated adenylyl cyclase OaPAC forming a homodimer. FMN: flavin mononucleotide, the light-absorbing pigment.  [ 1 ]


Bordered pits in the wood of  Picea abies . The top section is a cross-sectional view with bordered pits shown between adjacent cells, and the bottom section is a radial view with numerous bordered pits shown.


A simplified diagram of a simple pit pair


A simplified diagram of a bordered pit-pair with a torus and margo. The top shows an unobstructed pit and the bottom shows an aspirated pit, with the margo flexing under stress.


Cartoon representation of Planar Cell Polarity in fly wing hair cells and mouse paw hair cells Figure 1. (A and B)  Drosophila  cuticular wing hair cells of the adult wing. Wing hairs point distally (to the right) in wild-type (WT) animals (A) but lose orientation in PCP mutants ( fz ) (B). (C and D) Hairs on the mouse paw point away from the body (pointing up) in WT (C) but grow in a swirling pattern in PCP mutants ( fz6 ) (D). Inspired by the work of Paul Adler (A and B) and Guo et al. (2004) (C and D).


Figure 2: Cartoon representation of Cuticular wing hair defect in Frizzled mutant flies.(A) The structure of  Drosophila  fly wing with and arrow showing the proximal and distal tips, (B) WT cuticular hairs in normal orientation towards the distal tip of the wing, (C) the disoriented cuticular hairs of the Frizzled( fz)  mutant. The structures of the hairs are the same, only the orientation is different. Inspired by the work of David I. Strutt (2001)


An example plasmid with two areas of  antibiotic resistance  coding  DNA  (1,2) and an  origin of replication  (3).


Escherichia coli  bacteria on the right are sensitive to two beta-lactam antibiotics, and do not grow in the semi-circular regions surrounding the antibiotics.  E. coli  bacteria on the left are resistant to beta-lactam antibiotics, and grow next to one antibiotic ( bottom ) and are less inhibited by another antibiotic ( top ).


The  ligands , denoted by letter L, signal for platelets (P) to migrate towards the wound (Site A). As more platelets gather around the opening, they produce more ligands to amplify the response. The platelets congregate around the wound in order to create a cap to stop blood flow out of the tissue.


Platelets derive from multipotent marrow stem cells.


Platelets extruded from megakaryocytes


3D rendering of four inactivated and three activated platelets


Scanning electron micrograph of blood cells. From left to right: human  erythrocyte , activated platelet,  leukocyte .


Diagram of the structure of a platelet showing the granules


Platelet clumps in a blood smear


On for example optical densitometry, a first and second wave of platelet aggregation is seen, in this case for an  ADP -initiated aggregation.


Platelet concentrate


Platelets collected by using  apheresis  at an  American Red Cross  donation center


A  micrograph  showing cells with marked nuclear shape and size variation, a component of nuclear  pleomorphism .


Polyclonal response by B cells against linear epitopes [ 1 ]


Examples of substances recognized as foreign (non-self)


Schematic diagram to explain mechanisms of  clonal selection of B cell [ 8 ]


Steps in production of antibodies by B cells:   1.  Antigen is recognized and engulfed by B cell  2.  Antigen is processed  3.  Processed antigen is presented on B cell surface  4.  B cell and T cell mutually activate each other  5.  B cells differentiate into plasma cells to produce soluble antibodies


Recognition of conformational epitopes by B cells. Segments widely separated in the primary structure have come in contact in the three-dimensional tertiary structure forming part of the same epitope [ 1 ]


Steps of a macrophage ingesting a pathogen


Blind Monks Examining an Elephant : An  allegory  for the polyclonal response:  Each clone or antibody recognizes different parts of a single, larger antigen


The clone 1 that got stimulated by first antigen gets stimulated by second antigen, too, which best binds with naive cell of clone 2. However, antibodies produced by plasma cells of clone 1 inhibit the proliferation of clone 2. [ 21 ]


Frank Macfarlane Burnet  (1899-1985).


One super resolution study showed that Xist and PRC2 do not directly interact (above), while a second study showed that they are tightly and statistically significantly linked.


Post-translational modification of  insulin . At the top, the ribosome translates a mRNA sequence into a protein, insulin, and passes the protein through the  endoplasmic reticulum , where it is cut, folded, and held in shape by disulfide (-S-S-) bonds. Then the protein passes through the  golgi apparatus , where it is packaged into a vesicle. In the vesicle, more parts are cut off, and it turns into mature insulin.


Flowchart of the process and the data sources to predict PTMs. [ 26 ]


Effect of PTMs on protein function and physiological processes. [ 32 ]


Two  myeloblasts  with  Auer rods


Neural progenitors (green) in  olfactory bulb  with astrocytes (blue).


Example of the pattern of division of a progenitor cell (PC) which results in the production of an intermediate progenitor cell (IPC). Both cells later produce one or two neural cells (N).


Using a Beckman-Spinco Protein-Peptide Sequencer, 1970


Protein sequence interpretation: a scheme new protein to be engineered in a yeast


Sanger's method of peptide end-group analysis:  A  derivatization of  N -terminal end with  Sanger's reagent  (DNFB),  B  total acid hydrolysis of the dinitrophenyl peptide


A Beckman-Coulter Porton LF3000G protein sequencing machine


Circadian and ultradian rhythms of thyrotropin (TSH) concentration. Simulated time series created with  SimThyr .


Insulin release from the islet of Langerhans is pulsatile with a period of 3–6 minutes. [ 21 ]


Ragulator-Rag Complex, inactive.


Ragulator-Rag Complex, active


Ragulator complex with Lamtor 1 in green, Lamtor 2 in blue, Lamtor 3 in red, Lamtor 4 in yellow, Lamtor 5 in purple. ( PDB :  5Y39 )


Resin canals seen as white dots in pine tree viewed under a microscope


Axial resin canal ( Picea abies )


Pinus; leaf (3 needle type) Resin Canal


Model of the retromer heteropentameric complex ( VPS26  in green;  VPS35  in orange, and  VPS29  in red). The retromer forms a polymeric network arc on the outside (cytoplasmic side) of the endosome tubule. Inside the tubule, the cargo receptor  SORL1 , forms its own network and binds protein cargo for trafficking. SORL1 connects to retromer on the outside via a transmembrane helix and a short C-terminal tail that binds VPS26. Model built based on structural data by Brett Collins and Yu Kitago.


Ribbon diagram of the retromer heterotrimeric complex comprising the proteins VPS26 (green), VPS35 (orange) and VPS29 (red). On the endosomal membrane, this heterotrimer forms an arch-shaped dimer via interaction of two VPS35 molecules (see next image). [ 11 ]


CryoET structure of retromer heterotrimer dimer on the tubular endosome membrane in surface rendering. VPS26 is in green, VPS35 in orange, and VPS29 in red. The heterotrimer forms a characteristic dimeric arch. The grey SNX protein aids in tubulation and retromer membrane binding. [ 11 ]


Mechanisms of PMN rM


Neutrophil extracellular traps (NETs) in Sepsis


Chemokines and chemokine receptors in the neutrophil life cycle.


Model of a  woolly mammoth  at the  Royal BC Museum


Model depicting the calf "Dima", Stuttgart


Modern elephants are highly  gregarious , as shown by these  Sri Lankan elephants


An example of a ribonucleoprotein-motif protein. From  PDB  entry 1IBM.


ADAR  : an RNA binding protein involved in RNA editing events.


Diverse RNA contacts of RNA-binding proteins


" Zinc finger " : Cartoon representation of the zinc-finger motif of proteins. The zinc ion (green) is coordinated by two histidine and two cysteine amino acid residues.


Crawling  C. elegans  hermaphrodite worm


" CIRBP " : Structure of the CIRBP protein.


" Beta-actin " : Structure of the ACTB protein.


Branaplam Proposed Mechanism of Action.  Branaplam acts to promote exon 7 inclusion in SMA patients by enhancing splicing at the exon 7-exon 8 junction. The small molecule (NVS-SM2) enhances recognition of SMN2 transcripts by U1-U2 specifically by enhancing the affinity of U1 to the 5'-splice site of SMN exon 7. [ 13 ]


Small Molecule Drugs for the Treatment of Myotonic Dystrophy Type 1 (DM1).  Lead compounds for the treatment of Myotonic Dystrophy Type 1 (DM1) that recognize r(CUG)exp repeats in animal models and effect phenotypic outcomes consistent with the disease. PDB: 3GM7


NMR Structure of HIV-1 RNA frameshift site stem-loop bound to DB213, an inhibitor of viral replication. PDB: 2L94.


A cartoon section of  skeletal muscle , showing  T-tubules  running deep into the centre of the cell between two terminal cisternae/junctional SR. The thinner projections, running horizontally between two terminal cisternae are the longitudinal sections of the SR.


Porosome


Figure 1: Securin and separase are widely conserved


Figure 2: Five identified phosphorylation sites on securin


Figure 3: Network diagram with feedback loops to generate switch-like activation of anaphase


Figure 4: Potential network diagram involving securin to generate switch-like activation of anaphase


Self-assembly of  lipids  (a),  proteins  (b), and (c)  SDS - cyclodextrin  complexes. SDS is a  surfactant  with a hydrocarbon tail (yellow) and a SO 4  head (blue and red), while cyclodextrin is a  saccharide  ring (green C and red O atoms).


Transmission electron microscopy  image of an iron oxide  nanoparticle . Regularly arranged dots within the dashed border are columns of Fe atoms. Left inset is the corresponding  electron diffraction  pattern. Scale bar: 10 nm. [ 1 ]