Igf1r+/CD34+ immature ICC are putative adult progenitor cells, identified ultrastructurally as fibroblast-like ICC in Ws/Ws rat colon.

The colon of Ws/Ws mutant rats shows impairment of pacemaker activity and altered inhibitory neurotransmission. The present study set out to find structural correlates to these findings to resolve mechanisms. In the colon of Ws/Ws rats, interstitial cells of Cajal associated with Auerbach's plexus (ICC-AP) were significantly decreased and ICC located at the submuscular plexus and intramuscular ICC were rarely observed based on immunohistochemistry and electron microscopy. Ultrastructural investigations revealed that there was no overall loss of all types of interstitial cells combined. Where loss of ICC was observed, a marked increase in fibroblast-like ICC (FL-ICC) was found at the level of AP. Immunoelectron microscopy proved FL-ICC to be c-Kit(-) but gap junction coupled to each other and to c-Kit(+) ICC; they were associated with enteric nerves and occupied space normally occupied by ICC in the wild-type rat colon, suggesting them to be immature ICC. In addition, a marked increase in immunoreactivity for insulin-like growth factor 1 receptor (Igf1r) occurred, co-localized with CD34 but not with c-Kit. A significantly higher number of Igf1r(+)/CD34(+) cells were found in Ws/Ws compared to wild-type rat colons. These CD34(+)/Igf1r(+) cells in the Ws/Ws colon occupied the same space as FL-ICC. Hence we propose that a subset of immature ICC (FL-ICC) consists of adult progenitor cells. Immunohistochemistry revealed a reduction of neurons positive for neuronal nitric oxide synthase. The functional capabilities of the immature ICC and the regenerative capabilities of the adult progenitor cells need further study. The morphological features described here show that the loss of pacemaker activity is not associated with failure to develop a network of interstitial cells around AP but a failure to develop this network into fully functional pacemaker cells. The reduction in nitrergic innervation associated with the Ws mutation may be the result of a reduction in nitrergic neurons.

Severe inflammatory defect and reduced viability in CD18 and E-selectin double-mutant mice.

CD18-deficient mice (CD18(-/-) mice) have a severe leukocyte recruitment defect in some organs, and no detectable defect in other models. Mice lacking E-selectin (CD62E(-/-) mice) have either no defect or a mild defect of neutrophil infiltration, depending on the model. CD18(-/-)CD62E(-/-), but not CD18(-/-)CD62P(-/-), mice generated by crossbreeding failed to thrive, reaching a maximum body weight of 10-15 grams. To explore the mechanisms underlying reduced viability, we investigated lethally irradiated CD62E(-/-) mice that were reconstituted with CD18(-/-) bone marrow. These mice, but not single-mutant controls, showed tenfold-increased rolling velocities in a TNF-alpha-induced model of inflammation. Leukocyte adhesion efficiency in CD18(-/-)CD62E(-/-) mice was reduced by 95%, and hematopoiesis was drastically altered, including severe bone marrow and blood neutrophilia and elevated G-CSF and GM-CSF levels. The greatly reduced viability of CD18(-/-)CD62E(-/-) mice appears to result from an inability to mount an adequate inflammatory response. Our data show that cooperation between E-selectin and CD18 integrins is necessary for neutrophil recruitment and that alternative adhesion pathways cannot compensate for the loss of these molecules.

Study of exclusive charmless semileptonic B decays and |Vub|.

We study semileptonic B decay to the exclusive charmless states pi, rho/omega, eta, and eta;{'} using the 16 fb(-1) CLEO Upsilon(4S) data sample. We find B(B0-->pi-l+nu)=(1.37+/-0.15stat+/-0.11sys)x10(-4) and B(B0-->rho-l+nu)=(2.93+/-0.37stat+/-0.37sys)x10(-4) and find evidence for B+-->eta'l+nu, with B(B+-->eta'l+nu)=(2.66+/-0.80stat+/-0.56sys)x10(-4). From our B-->pilnu rate for q2>16 GeV2 and lattice QCD, we find |Vub|=(3.6+/0.4stat+/0.2syst-0.4thy+0.6)x10(-3) [corrected]

Low doses of ionizing radiation can prevent radiation-induced colonic epithelial hyporesponsiveness to muscarinic agonists.

PURPOSE: Colonic epithelium hyporesponsiveness to different secretagogues occurs after exposure to ionizing radiation, increasing susceptibility to bacterial translocation and intraluminal toxins. Growing evidence suggests that the biological effects of radiation might be hormetic in nature. We investigated if exposure to low doses of ionizing radiation (LDR) can prevent colon hyposecretion due to subsequent larger doses. METHODS: Rats were exposed to LDR (0.05 Gy) 24 h prior to 6 Gy, high dose radiation (HDR). The cyclic adenosine monophosphate (cAMP)-mediated pathway was explored using forskolin (FSK) and the intracellular Ca2+-mediated pathway through cholinergic stimulation. Changes in the colonic epithelium at the ultrastructural level were also explored. RESULTS: Maximal short circuit current (Isc) response to carbachol was significantly reduced in the group exposed to 6 Gy HDR and this was completely prevented by prior exposure to LDR. Responses to both FSK and electrical field stimulation (EFS) were significantly reduced after HDR but they were not prevented by prior adaption of LDR. Hyposecretion was not prevented by the inducible nitric oxide synthase (iNOS) inhibitor L-N6-(l-iminoethyl)lysine (L-NIL) ruling out a role for iNOS-derived nitric oxide (NO) in the colonic hyposecretion associated with whole body radiation. Prior exposure to LDR diminished the deleterious effect of full HDR on the ultrastructure of colonic epithelium as colonocytes vacuolization, microvilli lost and separation between neighboring cells were less evident. CONCLUSIONS: Previous exposure to LDR can prevent intracellular Ca2+-mediated colonic hyposecretion associated with exposure to HDR but fails to modify cAMP-mediated hyposecretion. Morphological damage at the ultrastructural level is less evident after prior LDR.

Potent inhibition of werner and bloom helicases by DNA minor groove binding drugs.

Maintenance of genomic integrity is vital to all organisms. A number of human genetic disorders, including Werner Syndrome, Bloom Syndrome and Rothmund-Thomson Syndrome, exhibit genomic instability with some phenotypic characteristics of premature aging and cancer predisposition. Presumably the aberrant cellular and clinical phenotypes in these disorders arise from defects in important DNA metabolic pathways such as replication, recombination or repair. These syndromes are all characterized by defects in a member of the RecQ family of DNA helicases. To obtain a better understanding of how these enzymes function in DNA metabolic pathways that directly influence chromosomal integrity, we have examined the effects of non-covalent DNA modifications on the catalytic activities of purified Werner (WRN) and Bloom (BLM) DNA helicases. A panel of DNA-binding ligands displaying unique properties for interacting with double helical DNA was tested for their effects on the unwinding activity of WRN and BLM helicases on a partial duplex DNA substrate. The levels of inhibition by a number of these compounds were distinct from previously reported values for viral, prokaryotic and eukaryotic helicases. The results demonstrate that BLM and WRN proteins exhibit similar sensitivity profiles to these DNA-binding ligands and are most potently inhibited by the structurally related minor groove binders distamycin A and netropsin (K(i)

Beta-bulges within loops as recurring features of protein structure.

Beta-bulges have been described as common irregularities in antiparallel beta-sheets. The two commonest kinds are described as 'classic' and 'G1'. The G1-type is often observed to occur at the loop end of beta-hairpins. I confirm this but also find that the characteristic G1 beta-bulge features (hydrogen bonds and dihedral angles) are found, in some loops, in the absence of any adjacent antiparallel beta-hairpin, so that the beta-bulge is effectively acting as a new sort of turn. Also I show that G1 beta-bulge loops occur in a number of different structural forms, some of which have not been described in detail before. G1 beta-bulge loops are common features; on average, a half of all proteins have one.

Predicting the biologically active conformations of short polypeptides.

In general, the smaller a polypeptide is, the less well defined its three-dimensional structure. In spite of advances in structure determination, the conformations of short polypeptides, as bound to their receptors, are not always easy to predict. However, much information about polypeptide structure is available from three-dimensional structures of proteins. James Milner-White discusses its relevance to small polypeptides and considers other means of inferring their biologically active conformations, especially for those that form loops and turns.

Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops.

A common feature of alpha-helices in proteins is a loop at the C-terminal end, with a characteristic hydrogen bond pattern. It is noted that several loops with the same structural features occur independently of alpha-helices; two are even situated at the loop ends of beta-hairpins. The name paperclip is suggested for loops possessing the appropriate hydrogen bonds. A number of features of paperclips are described: they exist in two classes, depending on the number of residues at the loop end; one class is very much commoner than the other. Two paperclips are found that belong to the common class, except that the main-chain conformation of each is the mirror image of that normally found. The majority of paperclips are shown to have tightly clustered sets of main-chain dihedral angles. These are somewhat similar to, but distinct from, a subgroup of another common family of loops that have been called beta-bulge loops; in the latter, the dihedral angles are also tightly clustered. The high degree of clustering in both cases is likely to be a result of steric constraints associated with hydrogen bond patterns at the ends of loops.

Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites.

Gamma-turns occur as one of two possible enantiomers with regard to their main-chain structure, called classic and inverse. Of these, inverse ones are more common. Unlike other hydrogen bonds, those in inverse gamma-turns include a large proportion that are weak. If such hydrogen bonds are included, these turns may be said to be abundant in proteins. A significant number of inverse gamma-turns, usually weak ones, exist as consecutive turns in a structural feature, now called the 2.2(7)-helix, proposed for polypeptides as long ago as 1943 by Huggins. Most of these features occur within strands of beta-sheet. The less-weak inverse gamma-turns fall into several structural subgroups. They are frequently situated directly at either end of alpha-helices or of strands of beta-sheet, or adjacent to certain loop motifs. In general, they are well conserved during evolution and some are found at key positions in proteins. One occurs in the first hypervariable loop in the heavy chain of immunoglobulins.

The N-terminal domain of MDM2 resembles calmodulin and its relatives.

It is shown here that the N-terminal domain of MDM2, which is not thought to bind calcium ions, otherwise bears a striking resemblance to a cluster of four EF-hand modules like those found in the calmodulin family. There are similarities in module arrangement, supersecondary structure and the main-chain to main-chain hydrogen-bonding pattern, especially in the vicinity of the short antiparallel beta-sheet, the two strands of which lie between the two E and F helices of tandem modules. Some conserved amino acid residues are identified that are associated with short side-chain to main-chain hydrogen-bonded motifs. Also, both types of domain bind a short, functionally important hydrophobic alpha-helix from another protein in a cavity between the two pairs of EF-hand, or EF-hand-like, modules.

A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations.

Examination of the ways side-chain carboxylate and amide groups in high-resolution protein crystal structures form hydrogen bonds with main-chain atoms reveals that the most common category is a two-hydrogen-bond four to five residue motif with an aspartate or asparagine (Asx) at the first residue, for which we propose the name Asx-motif. Similar motifs with glutamate or glutamine residues at that position are rare. Asx-motifs occur typically as (1) a common feature of the N termini of alpha-helices called the Asx N-cap motif; (2) an independent motif, usually a beta-turn with an appropriately hydrogen-bonded Asx as the first residue; and (3) a motif incorporated in a beta-bulge loop. Asx-motifs are common, there being just under two-and-a-half in an average-sized protein subunit; of these, about 55 % are Asx N-cap motifs. Because they occur often in many situations, it seems that these motifs have an inherent propensity to form on their own rather than just being a feature stabilised at the end of a helix. Asx-motifs also occur in functionally interesting situations in aspartyl proteases, citrate synthase, EF hands, haemoglobins, lipocalins, glutathione reductase and the alpha/beta hydrolases.

A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations.

Side-chain hydroxyl residues in protein crystal structures often form hydrogen bonds with main-chain atoms. The most common bond arrangement is a four to five residue motif in which a serine or threonine is the first residue forming two characteristic hydrogen bonds to residues ahead of it in sequence. We call them ST-motifs, by analogy with the term Asx-motif we suggested for the related motifs with aspartate and asparagine residues. ST-motifs are common, there being just under one and a half in a typical protein subunit. Asx-motifs are even more common, such that 9 % of the residues of an average protein consist of Asx or ST-motifs. Of the ST-motifs, three-quarters are at helical N termini, and the rest occur by themselves or in conjunction with beta-bulge loops. A third of all alpha-helices have either ST-motifs or Asx-motifs at their N termini. Previous work has emphasised the occurrence of the capping box at alpha-helical N termini, but the capping box occurs in only 5 % of alpha-helical N termini; also, we point out that it can be regarded as a subset of the ST-motif (or, occasionally, of the Asx-motif). By comparing related sequences, the rates which amino acid residues at the first position of ST or Asx-motifs interchange during evolution are examined. Serine <==> threonine, and aspartate <==> asparagine, interchange is rapid; inter-pair exchange is slower, but much faster than exchange with other amino acid residues. This is consistent with the general similarity of ST-motifs and Asx-motifs combined with some subtle structural differences between them that are described.

Evidence for an ancestral core structure in nucleotide-binding proteins with the type A motif.

Many proteins that bind purine nucleotide triphosphates have a type A sequence motif. Only two classes of structures for such proteins are so far available from X-ray crystallography. We examined the tertiary structures of representatives of the two classes, porcine cytoplasmic adenylate kinase and Escherichia coli translational elongation factor Tu. Comparison of the two proteins suggests that the A motif may be just one part of a larger common core structure consisting of four parallel strands of beta-sheet sandwiched between four alpha-helices. This compact core structure comprises over one half of each protein. We speculate that A motif proteins have diverged from a common ancestor having this core structure.

Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions.

An angle named gamma has been employed to describe the geometry at a hydrogen bond between main-chain atoms of polypeptides. In antiparallel beta-sheet, gamma is normally positive, whereas, in parallel beta-sheet and alpha-helices, it is negative. Although intriguing, no particular explanation has been offered to explain this result. We provide evidence that, in each case, the angular preference maximises the favourable Coulombic interaction between the partial negative charge on the carbonyl oxygen atom and the partial positive charge on the carbonyl carbon atom adjacent to the NH group to which it is hydrogen-bonded. Analyses of helices and beta-sheets in native proteins using Lennard-Jones potentials suggest that these carbonyl-carbonyl interactions are significant components of the attractive forces holding main-chain CONH groups together and are even in some cases larger than the hydrogen bonds themselves. A novel technique for analysing the forces holding together hydrogen-bonding groups in proteins is presented. It can be regarded as a development of the Kabsch and Sander method of calculating the energy of hydrogen bonds between main-chain atoms. In their program, electrostatic interactions are calculated between appropriate pairs of atoms, i.e. NH binding to CO. Instead, in our method, the four N, H, C, and O atoms, in a peptide bond are taken as a unit and the interaction between two NHCO groups calculated. We also use a Lennard-Jones potential, rather than just measuring the Coulombic interaction. With this approach, account is taken of all types of interactions between partially charged atoms, not only the hydrogen bonds.

Coulombic attractions between partially charged main-chain atoms stabilise the right-handed twist found in most beta-strands.

The use of Lennard-Jones potentials gives rise to an expected energy distribution for main-chain polypeptide conformations in the Ramachandran plot that matches well the observed distribution of phi, psi values in high-resolution proteins. The position of the energy minimum in the beta-strand conformation region is situated where there is a substantial contribution from the electrostatic attraction between the partial charge of the carbonyl carbon atom of one amino acid residue and that of the carbonyl oxygen atom of an adjacent residue. This attraction gives rise to a preference for the right-twisted beta-strand conformation compared with the left-twisted conformation. The majority of beta-sheets are twisted, almost always in one direction. Looking along a single strand, the twist is to the right. This twist also helps provide a rationale for the characteristic topology of the strand-helix-strand unit often observed in alpha/beta proteins. The electrostatic explanation for the twist we propose has not, to our knowledge, been explicitly suggested previously. The factor that has been most widely proposed to explain the twist is steric hindrance involving side-chain atoms. We provide evidence that the electrostatic effect is of comparable significance. Right-twisted beta-strands are geometrically closely related to polyproline II helices and to collagen helices, both of which are left-handed. Short regions of polyproline II type helices, which are sometimes, but not always, rich in proline residues, are common at protein surfaces. We point out that these helices are stabilised by the same carbonyl-carbonyl interactions as in right-twisted beta-strands.

Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides. Different puckers are favoured in certain situations.

In a set of proteins studied at high resolution by X-ray crystallography over a half of all cis and trans-proline residues could be unambiguously assigned to one of the two forms of pyrrolidine ring puckering, called UP and DOWN. Of these, 89% of the cis-proline residues exhibit the DOWN pucker, while the trans-proline residues, on average, are about evenly distributed between the two forms. Of trans-proline residues found in alpha-helices, 79% have the UP ring pucker. trans-proline residues occurring in other situations are more equally distributed between the two forms of pucker, although further generalizations may be possible. Proline residues in a set of crystal structures of short polypeptides were also examined. As in the protein sample, a tendency for the cis-proline residues to have the DOWN pucker was observed, but the effect was less pronounced.

Common ring motifs in proteins involving asparagine or glutamine amide groups hydrogen-bonded to main-chain atoms.

We report the frequent occurrence in proteins of motifs consisting of either 9-membered or 11-membered rings that involve the side-chain amide groups of asparagine and glutamine residues. The syn CO and NH groups of these amide groups are hydrogen-bonded to the main-chain NH and CO groups of other amino acid residues. The main-chain part of both the 9-membered and 11-membered rings has the conformation of a beta-strand. One such ring motifs occurs, on average, in half of all the proteins we examined. Similar conformations are found for most examples of the 9-membered and 11-membered rings. One of the 11-membered rings is distinct, compared to the others, in that its main-chain part has a mirror-image conformation. Another of the 11-membered rings occurs at the interior of the variable domains of some antibodies and assists in linking the two beta-sheets. We observe one 9-membered ring structure in a dihydrofolate reductase complex in which the amide in the nicotinamide group of the ligand NADP is bound to the enzyme. Groups that can form hydrogen bonds in a similar way to amide groups occur in several nucleotide bases; we find one example of a 9-membered ring involving adenine and main-chain atoms in the FAD-protein complex of glutathione reductase. Both have conformations like those of the other 9-membered rings.

Plasticity of glomeruli and olfactory-mediated behavior in zebrafish following detergent lesioning of the olfactory epithelium.

The zebrafish olfactory system is a valuable model for examining neural regeneration after damage due to the remarkable plasticity of this sensory system and of fish species. We applied detergent to the olfactory organ and examined the effects on both morphology and function of the olfactory system in adult zebrafish. Olfactory organs were treated once with Triton X-100 unilaterally to study glomerular innervation patterns or bilaterally to study odor detection. Fish were allowed to recover for 4-10 days and were compared to untreated control fish. Axonal projections were analyzed using whole mount immunocytochemistry with anti-keyhole limpet hemocyanin, a marker of olfactory axons in teleosts. Chemical lesioning of the olfactory organ with a single dose of Triton X-100 had profound effects on glomerular distribution in the olfactory bulb at 4 days after treatment, with the most significant effects in the medial region of the bulb. Glomeruli had returned by 7 days post-treatment. Analysis of the ability of the fish to detect cocktails of amino acids or bile salts consisted of counting the number of turns the fish made before and after odorant delivery. Control fish turned more after exposure to both odorants. Fish tested 4 and 7 days after chemical lesioning made more turns in response to amino acids but did not respond to bile salts. At 10 days post-lesion, these fish had regained the ability to detect bile salts. Thus, the changes seen in bulbar innervation patterns correlated to odorant-mediated behavior. We show that the adult zebrafish brain has the capacity to recover rapidly from detergent damage of the olfactory epithelium, with both glomerular distribution and odorant-mediated behavior returning in 10 days.

C-Jun N-terminal kinases are required for oncolytic adenovirus-mediated autophagy.

Oncolytic adenoviruses, such as Delta-24-RGD (Δ24RGD), are replication-competent viruses that are genetically engineered to induce selective cancer cell lysis. In cancer cells, Δ24RGD induces massive autophagy, which is required for efficient cell lysis and adenoviral spread. Understanding the cellular mechanisms underlying the regulation of autophagy in cells treated with oncolytic adenoviruses may provide new avenues to improve the therapeutic effect. In this work, we showed that cancer cells infected with Δ24RGDundergo autophagy despite the concurrent activation of the AKT/mTOR pathway. Moreover, adenovirus replication induced sustained activation of JNK proteins in vitro. ERK1/2 phosphorylation remained unchanged during adenoviral infection, suggesting specificity of JNK activation. Using genetic ablation and pharmacological inactivation of JNK, we unequivocally demonstrated that cells infected with Δ24RGD required JNK activation. Thus, genetic co-ablation of JNK1 and JNK2 genes or inhibition of JNK kinase function rendered Δ24RGD-treated cells resistant to autophagy. Accordingly, JNK activation induced phosphorylation of Bcl-2 and prevented the formation of Bcl-2/Beclin 1 autophagy suppressor complexes. Using an orthotopic model of human glioma xenograft, we showed that treatment with Δ24RGD induced phosphorylation and nuclear translocation of JNK, as well as phosphorylation of Bcl-2. Collectively, our data identified JNK proteins as an essential mechanistic link between Δ24RGD infection and autophagy in cancer cells. Activation of JNK without inactivation of the AKT/mTOR pathway constitutes a distinct molecular signature of autophagy regulation that differentiates Δ24RGD adenovirus from the mechanism used by other oncolytic viruses to induce autophagy and provides a new rationale for the combination of oncolytic viruses and chemotherapy.

The partial charge of the nitrogen atom in peptide bonds.

A majority of the standard texts dealing with proteins portray the peptide link as a mixture of two resonance forms, in one of which the nitrogen atom has a positive charge. As a consequence, it is often believed that the nitrogen atom has a net positive charge. This is in apparent contradiction with the partial negative charge on the nitrogen that is used in force fields for molecular modeling. However, charges on resonance forms are best regarded as formal rather than actual charges and current evidence clearly favors a net negative charge for the nitrogen atom. In the course of the discussion, new ideas about the electronic structure of amides and the peptide bond are presented.