Intrinsic disorder controls two functionally distinct dimers of the master transcription factor PU.1

Transcription factors comprise a major reservoir of conformational disorder in the eukaryotic proteome. The hematopoietic master regulator PU.1 presents a well-defined model of the most common configuration of intrinsically disordered regions (IDRs) in transcription factors. We report that the structured DNA binding domain (DBD) of PU.1 regulates gene expression via antagonistic dimeric states that are reciprocally controlled by cognate DNA on the one hand and by its proximal anionic IDR on the other. The two conformers are mediated by distinct regions of the DBD without structured contributions from the tethered IDRs. Unlike DNA-bound complexes, the unbound dimer is markedly destabilized. Dimerization without DNA is promoted by progressive phosphomimetic substitutions of IDR residues that are phosphorylated in immune activation and stimulated by anionic crowding agents. These results suggest a previously unidentified, nonstructural role for charged IDRs in conformational control by mitigating electrostatic penalties that would mask the interactions of highly cationic DBDs.

Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1

Functional evidence increasingly implicates low-affinity DNA recognition by transcription factors as a general mechanism for the spatiotemporal control of developmental genes. Although the DNA sequence requirements for affinity are well-defined, the dynamic mechanisms that execute cognate recognition are much less resolved. To address this gap, here we examined ETS1, a paradigm developmental transcription factor, as a model for which cognate discrimination remains enigmatic. Using molecular dynamics simulations, we interrogated the DNA-binding domain of murine ETS1 alone and when bound to high-and low-affinity cognate sites or to nonspecific DNA. The results of our analyses revealed collective backbone and side-chain motions that distinguished cognate versus nonspecific as well as high- versus low-affinity cognate DNA binding. Combined with binding experiments with site-directed ETS1 mutants, the molecular dynamics data disclosed a triad of residues that respond specifically to low-affinity cognate DNA. We found that a DNA-contacting residue (Gln-336) specifically recognizes low-affinity DNA and triggers the loss of a distal salt bridge (Glu-343/Arg-378) via a large side-chain motion that compromises the hydrophobic packing of two core helices. As an intact Glu-343/Arg-378 bridge is the default state in unbound ETS1 and maintained in high-affinity and nonspecific complexes, the low-affinity complex represents a unique conformational adaptation to the suboptimization of developmental enhancers.

ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma

Recurrent mutations are frequently associated with transcription factor (TF) binding sites (TFBS) in melanoma, but the mechanism driving mutagenesis at TFBS is unclear. Here, we use a method called CPD-seq to map the distribution of UV-induced cyclobutane pyrimidine dimers (CPDs) across the human genome at single nucleotide resolution. Our results indicate that CPD lesions are elevated at active TFBS, an effect that is primarily due to E26 transformation-specific (ETS) TFs. We show that ETS TFs induce a unique signature of CPD hotspots that are highly correlated with recurrent mutations in melanomas, despite high repair activity at these sites. ETS1 protein renders its DNA binding targets extremely susceptible to UV damage in vitro, due to binding-induced perturbations in the DNA structure that favor CPD formation. These findings define a mechanism responsible for recurrent mutations in melanoma and reveal that DNA binding by ETS TFs is inherently mutagenic in UV-exposed cells.

Many factors contribute to mutation hotspots in cancer cells. Here the authors map UV damage at single-nucleotide resolution across the human genome and find that binding sites of ETS transcription factors are especially prone to forming UV lesions, leading to mutation hotspots in melanoma.

Multiple DNA-binding modes for the ETS family transcription factor PU.1

The eponymous DNA-binding domain of ETS (E26 transformation-specific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA-binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. Whereas 10 bp of DNA was sufficient to support PU.1 binding as a monomer, additional flanking bases were required to invoke sequential dimerization of the bound protein. NMR spectroscopy revealed a marked loss of signal intensity in the 2:1 complex, and mutational analysis implicated the distal surface away from the bound DNA as the dimerization interface. Hydroxyl radical DNA footprinting indicated that the site-specifically bound PU.1 dimers occupied an extended DNA interface downstream from the 5'-GGAA-3' core consensus relative to its 1:1 counterpart, thus explaining the apparent site size requirement for sequential dimerization. The site-specifically bound PU.1 dimer resisted competition from nonspecific DNA and showed affinities similar to other functionally significant PU.1 interactions. As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level.

Distinct Roles for Interfacial Hydration in Site-Specific DNA Recognition by ETS-Family Transcription Factors

The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. Unlike other ETS homologues, such as Ets-1, DNA recognition by PU.1 is highly sensitive to its osmotic environment due to excess interfacial hydration in the complex. To investigate interfacial hydration in the two homologues, we mutated a conserved tyrosine residue, which is exclusively engaged in coordinating a well-defined water contact between the protein and DNA among ETS proteins, to phenylalanine. The loss of this water-mediated contact blunted the osmotic sensitivity of PU.1/DNA binding, but did not alter binding under normo-osmotic conditions, suggesting that PU.1 has evolved to maximize osmotic sensitivity. The homologous mutation in Ets-1, which was minimally sensitive to osmotic stress due to a sparsely hydrated interface, reduced DNA-binding affinity at normal osmolality but the complex became stabilized by osmotic stress. Molecular dynamics simulations of wildtype and mutant PU.1 and Ets-1 in their free and DNA-bound states, which recapitulated experimental features of the proteins, showed that abrogation of this tyrosine-mediated water contact perturbed the Ets-1/DNA complex not through disruption of interfacial hydration, but by inhibiting local dynamics induced specifically in the bound state. Thus, a configurationally identical water-mediated contact plays mechanistically distinct roles in mediating DNA recognition by structurally homologous ETS transcription factors.

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacyl intermediate and an NAD⁺-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp³-to-sp² transition during enzyme-mediated oxidation.

Aldehydes are common intermediates in enzymatic pathways, but their high reactivity can make them difficult to observe. Here, the authors study the mechanism of aldehyde deactivation in a dehydrogenase, showing a key E/Z isomerization and observing a thiohemiacetal intermediate by crystal structure analysis.

Hepatocyte growth factor incorporated into herpes simplex virus vector accelerates facial nerve regeneration after crush injury

Hepatocyte growth factor (HGF) promotes regeneration of the central nervous system, but its effects on the peripheral nervous system remain unclear. This study was conducted to elucidate the effect of HGF on regeneration of the murine facial nerve after crush injury. To do so, a replication-defective herpes simplex virus vector that incorporated HGF was prepared (HSV-HGF). The main trunk of the facial nerve was compressed by mosquito hemostats, and HSV-HGF, control vector or medium was then applied to the compressed nerve. We found that mice in the HGF group required significantly fewer days for complete recovery from nerve compression. Furthermore, the amplitude of the evoked buccinator muscle compound action potential increased following HSV-HGF application. HGF expression in and around the compressed nerve was demonstrated by enzyme-linked immunoassay and immunohistochemistry. In addition, HSV-HGF introduction around the damaged nerve significantly accelerated recovery of function of the facial nerve. These data suggest a possible role of HGF in promoting facial nerve regeneration after nerve damage. Furthermore, this viral delivery method may be applied clinically for many types of severe facial palsy during facial nerve decompression surgery.

Single-motor mechanics and models of the myosin motor

Recent progress in single-molecule detection techniques is remarkable. These techniques have allowed the accurate determination of myosin-head-induced displacements and how mechanical cycles are coupled to ATP hydrolysis, by measuring individual mechanical events and chemical events of actomyosin directly at the single-molecule level. Here we review our recent work in which we have made detailed measurements of myosin step size and mechanochemical coupling, and propose a model of the myosin motor.

Single molecule analysis of the actomyosin motor

Progress in imaging techniques and nano-manipulation of single molecules has been remarkable. These techniques have allowed the accurate determination of myosin-head-induced displacements and of how the mechanical cycles of the actomyosin motor are coupled to ATP hydrolysis. This has been achieved by measuring mechanical and chemical events of actomyosin directly at the single molecule level. Recent studies have made detailed measurements of myosin step size and mechanochemical coupling. The results of these studies suggest a new model for the mechanism of motion underlying actomyosin motors, which differs from the currently accepted lever-arm swinging model.

Laparoscopic surgery in newborn infants

BACKGROUND

Thanks to various technical innovations and advances in instrumentation, laparoscopic surgical intervention is now possible for certain congenital anomalies in children. To test the applicability of laparoscopic surgery in neonates, we reviewed our personal experience of neonatal laparoscopic surgery, focusing on cardiopulmonary function, surgical procedures, problems with devices, and degree of associated surgical stress.

METHODS

We performed 65 laparoscopic procedures in neonates. Their ages ranged from 2 to 30 days old, and their body weights ranged from 1,980 to 4,780 g. All 65 laparoscopic procedures were carried out without mortality or serious morbidity.

RESULTS

As complications, we encountered four cases of hypothermia due to rapid insufflation of carbon dioxide (CO(2)). We also found that relative hypercapnea (increase in end-tidal CO(2) as high as 61 mmHg) developed unless hyperventilation and a relatively high peak insufflation pressure were maintained during pneumoperitoneum. No cardiac depression developed at this insufflation pressure. Fluid and electrolyte balance during our cases of newborn laparoscopic surgery, as well as the doses and volumes of fluid and electrolytes administered, were identical to those required for open surgery. Interleukin-6 (IL-6) was measured serially to estimate the degree of associated surgical stress and was found to be significantly lower in neonates who had received laparoscopic procedures than in those who had received open procedures.

CONCLUSION

Laparoscopic surgery can be carried out safely even in neonates.

Laparoscopic extramucosal pyloromyotomy versus open pyloromyotomy for infantile hypertrophic pyloric stenosis: which is better?

BACKGROUND/PURPOSE

The aim of this study was to evaluate the advantages or disadvantages of laparoscopic pyloromyotomy compared with open transumbilical fold pyloromyotomy.

METHODS

Thirty consecutive laparoscopic extramucosal pyloromyotomies (LP) performed from 1994 to 1997 were compared with 30 consecutive open pyloromyotomies (OP) performed during the same period with regard to age at operation, body weight, thickness of hypertrophied pyloric muscle, operating time, time of return to full feeding, frequency of postoperative emesis, surgical complications, and degree of surgical stress reflected by interleukin-6 (IL-6). LP was performed according to conventional techniques, and OP was performed using a transumbilical fold approach.

RESULTS

The groups were matched for age at operation, preoperative clinical and physical status, laboratory data, and size of the hypertrophied pylorus assessed by ultrasonography. There was a learning curve with LP; the average operating time required for the first 10 cases was significantly longer than the time required for OP, but later cases took just as long as OP cases. Time taken to full feeding was significantly shorter in the LP group than the OP group (LP, 38 hours v OP, 64 hours). One case was converted from LP to OP because of mucosal perforation. The incidence of postoperative emesis was significantly higher in the OP group than in the LP group (OP, 25% v LP, 3%). The mean length of hospitalization was significantly shorter in LP (P < .01). The intraoperative peak values of IL-6 in LP were significantly lower than those in the OP group (P < .01).

CONCLUSIONS

The advantages of LP are improved cosmesis, decreased surgical stress with earlier postoperative recovery, and shorter hospitalization. Because LP uses reusable devices, and the mean period of hospitalization is shorter, average operating costs could be reduced, representing a net saving in total hospital charges.

Immunosuppression by anti-ICAM-1 and anti-LFA-1 monoclonal antibodies of free and vascularized skin allograft rejection

Immunosuppression by anti-adhesion molecule antibody of free or vascularized skin allograft rejection was investigated in rats. Lewis (LEW, RT11) rats were used as donors and Fisher (F344, RT11v1) rats as the recipients. When F344 rats were treated intraperitoneally (i.p.) with anti-intercellular adhesion molecule-1 (ICAM-1) mAb (1A29) (3 mg/kg/day) and anti-leukocyte function-associated antigen-1 (LFA-1) mAb (WT.1) (3 mg/kg/day) one day prior to grafting and daily after grafting for nine days, free skin graft survival was prolonged only slightly compared with that in control rats which were injected i.p. with a daily dose of 6 mg/kg of anti-TNP mAbs (H1-6-2) one day prior to grafting and daily after grafting for nine days. (Mean survival time [MST] of the free skin graft was 11.2 +/- 0.6 days in the control group and 13.4 +/- 0.3 days in the 1A29 + WT-1 treated group [p < 0.01], respectively.) On the other hand, the vascularized graft survival was prolonged significantly in anti-ICAM-1/LFA-1 mAbs-treated F344 rats as compared with that in control rats. (The mean vascularized graft survival time was 14.2 +/- 0.7 days in the control group and 21.5 +/- 1.9 days in 1A29 + WT-1 treated group [p < 0.002]). Our results suggest that interaction with ICAM-1 and LFA-1 is more important in the rejection of vascularized skin allografts than that of free skin allografts.

Protein glycation inhibitors from thyme (Thymus vulgaris)

Nonenzymatic glycation of bovine serum albumin (BSA) was inhibited in vitro by some extracts of 34 kinds of spices. The methanol extract of thyme (Thymus vulgaris) had the most potent inhibitory activity among them. Chromatographic purification yielded four flavonoids, quercetin (1), eriodictyol (2), 5,6,4'-trihydroxy-7,8,3'-trimethoxyflavone (3), and cirsilineol (4). These known flavonoids suppressed the levels of advanced glycation end products (AGEs) and fructosamines, shown by the measurement of specific fluorescent groups and the reduction of nitroblue tetrazolium (NBT), respectively. The inhibitory activities were compared with those of other structure-related flavonoids and aminoguanidine.

Radioprotective effect of antioxidative flavonoids in gamma-ray irradiated mice

The anticlastogenic effect of 12 structurally different flavonoids was investigated in whole body gamma-ray irradiated mice. Each flavonoid was administered to ICR male mice by a single gastric intubation (5 mumol/kg) 6 h before gamma-ray irradiation (1.5 Gy) and the frequency of micronucleated reticulocytes (MNRETs) in peripheral blood was determined. In order to elucidate the mechanism of the anticlastogenic effect of these flavonoids, their antioxidative activities were examined by the thiobarbituric acid method using methyl linoleate and Fenton's reagent (Fe2+/H2O2). Of the 12 flavonoids, luteolin had the most marked effect on reducing the frequencies of MNRETs and also inhibiting lipid peroxidation. However, quercetin tetramethylether, which has methoxy groups instead of hydroxyl groups at the 3,7,3',4'-positions, and phloretin with an open C-ring showed the least anticlastogenic and antioxidative activity. A good correlation (r = 0.717, P < 0.01) was observed between the anticlastogenic activity and the antioxidative activity of the 12 flavonoids. These results suggest that the radioprotective effect of flavonoids in mice may be attributed to the hydroxyl radical scavenging potency in a direct or an endogenous enzyme mediated manner.

Preparation and taste of certain glycosides of flavanones and of dihydrochalcones

The 7-O-[2-O-(alpha-L-Rhamnopyranosyl)-beta-L-quinovoside] of naringenin and of hesperetin, and their dihydrochalcone (DHC) derivatives were synthesized by the method of Koenigs-Knorr (Ag2CO3 and quinoline). The reaction of TMS ethers of naringenin and of hesperetin with each of the alpha-acetofluoro derivatives of D-glucose, L-rhamnose, 2-O-(alpha-L-rhamnopyranosyl)-L-rhamnose, and 2-O-(alpha-L-rhamnopyranosyl)-D-glucose (neohesperidose), using boron trifluoride etherate as an activator, yielded coupling products which, after deprotection, gave naringenin 4'-O-beta-D-glucoside, naringenin 4'-O-alpha-L-rhamnoside, naringenin 4'-O-[2-O-(alpha-L-rhamnopyranosyl)-alpha-L-rhamnoside], hesperetin 3'-O-[2-O-(alpha-L-rhamnopyranosyl)-alpha-L-rhamnoside], and naringenin 4'-O-beta-neohesperidoside, respectively. Catalytic hydrogenation of these flavanones gave the corresponding DHC derivatives. Hesperetin DHC 4'-O-[2-O-(alpha-L-rhamnopyranosyl-beta-L-quinovoside] was 300 times sweeter than sucrose, while the other compounds were bitter or tasteless.

The distally based superficial sural artery flap

The distally based superficial sural artery flap, first described as a distally based neuroskin flap by Masquelet et al., is a skin island flap supplied by the vascular axis of the sural nerve. The aim of this paper is to refine the surgical technique in order to establish the reliability of this flap. We treated 20 patients with 21 distally based superficial sural artery flaps, including 2 fascial flaps. All flaps survived. Most flaps showed slight venous congestion. In the largest flap (10 cm wide by 13 cm long), edema lasted 2 months. In the flap whose pedicle was raised without the deep fascia, there was necrosis at the distal tip of the flap. The advantages are the following: The blood supply is reliable, elevation is easy and quick, and major arteries are not sacrificed. This new flap may be useful in selected circumstances.

Synthesis of alpha-L-mannopyranosyl-containing disaccharides and phenols as substrates for the alpha-L-mannosidase activity of commercial naringinase

In order to clarify the substrate specificity of the alpha-L-mannosidase activity of naringinase (Sigma), the following disaccharides and phenol glycosides were freshly prepared: methyl 2-O-(alpha-L-mannopyranosyl)-beta-D-glucoside (1), methyl 3-O-(alpha-L-mannopyranosyl)-alpha-D-glucoside (2), methyl 4-O-(alpha-L-mannopyranosyl)-alpha-D-glucoside (3), methyl 5-O-(alpha-L-mannopyranosyl)-beta-D-glucoside (4), methyl 6-O-(alpha-L-mannopyranosyl)-alpha-D-glucoside (5), 6-O-(alpha-L-mannopyranosyl)-D-galactose (6), p-nitrophenyl alpha-L-mannoside (7), and 4-methyl umbelliferone alpha-L-mannoside (8). These compounds, except for 3 and 5 were hydrolyzed with naringinase.

Effect of middle ear infection on pneumatization and growth of the mastoid process. An experimental study in pigs

The intention of this experiment was to investigate whether anatomical variations of the temporal bone such as low middle fossa dura, anterior position of the sigmoid sinus or small mastoid process, which are often seen at surgery in cholesteatoma patients, are caused by inflammation in early childhood. In 7 pigs, 1.5 ml paraffin liquid were instilled into the left tympanic cavity 2 or 7 days after birth in order to produce inflammation of the middle ear and tubal dysfunction. After six and a half months the length and area of the mastoid process were significantly smaller on the left instilled side than on the right, normal side. In all cases there was remarkable hypocellularity and increased thickness of the cortical bone strongly supporting the environmental theory of pneumatization that inflammation suppresses the pneumatization process and growth of the mastoid process.

[The size of the mastoid pneumatization and otitis media with effusion in children]

It is generally believed that a cause and effect relationship exists between chronic middle ear inflammatory conditions and suppressed growth of the pneumatized cellulae. We already demonstrated the normal process of pneumatization and the suppressive process of pneumatization in experimental studies using pigs. In that study, the process of suppression of the pneumatization was caused by the continuous inflammatory changes of the epithelium of the middle ear cavity, and the degree of the suppression of the pneumatization was caused by the degree and duration of the air cavity's inflammatory condition at the growing stage of the mastoid process. We also carried out the histological study of the normal process of pneumatization using 100 sides of human fetuses between 16th and 36th week of pregnancy. In these studies the bone metabolisms which were found in the normal processes of pneumatization in pigs and human fetuses were same, and the normal pneumatization occurred at the growing stage of the mastoid process. This growing period of the mastoid is from 0 to 6 months after birth in pigs, and 0 to 15 years in humans. So in humans, we can infer that the suppression of the growth of the cellulae is closely related to a persistent state of otitic inflammation like an otitis media with effusion in the early stages of growth. From these studies, in children who have otitis media with effusion, it will be possible to realize the previous middle ear pathology by the degree of the suppression of pneumatization on x-ray film.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of middle ear infection upon the pneumatization of the mastoid: an experimental study in pigs

The suppression of the temporal bone's pneumatized cavities is commonly observed in chronic middle ear inflammatory disease, but this fact has not been explained in respect to its etiology, i.e., whether the poorly pneumatized cavity induces chronic middle ear infection or middle ear inflammatory condition suppresses the pneumatization of cellulae. We studied the effect of middle ear infection and eustachian tubal dysfunction in the early stage of life upon the development of pneumatization of the mastoid using 13 pigs, whose mastoid is comparable to that of man. We used two methods, the eustachian tube stenosis test and the tympanic membrane paraffin infusion test. The present study indicated that in six pigs infection of the middle ear in the early stage of life suppressed the normal development of pneumatization of the mastoid bone in pigs.

Bacterial examination of serous otitis media and experimental tubal stenosis

Involvement of bacteria in serous otitis media was studied in man and by animal experimentation (using rabbits). Bacteria from the middle ear fluid, the skin of the external ear canal and the epipharynx of 100 human ears were cultured. Bacteria were also cultured from 50 ears of rabbits with serous otitis media induced experimentally by tubal stenosis, in the same way as those taken from human ears. Bacteria were detected in the middle ear fluid of 61 human ears (61%), and in 48 human ears (48%) except for those with contamination. The bacteria detected in the middle ear fluid were the same as those detected in the epipharynx in 40 of the 50 rabbit ears during the period from the start of treatment to the 30th day. In ears which were treated for more than 30 days, the bacteria detected in the middle ear fluid tended not to be the same as those detected in the epipharynx. From these results it was inferred that inflammation of the epipharynx spread over the middle ear cavity through the auditory tube.

[Pharmacokinetics of cisplatin and the effect of sodium thiosulfate]

The pharmacokinetics of cisplatin (cis-dichlorodiammineplatinum (II), CDDP) have been studied in 11 patients. Plasma and urine CDDP concentrations were determined by flameless atomic absorption spectrophotometry. The treatment schedule was administered either by a 3-hour and 4-hour i.v. infusion or a 1.5-hour i.a. infusion. In the 3-hour i.v. infusion, the peak level of plasma total CDDP was 4.09 micrograms/ml after the end of infusion and non-protein-bound CDDP was 0.78 microgram/ml. Plasma total CDDP level declined with two peaks, the half-life of the alpha phase being 3.3 hours and that of the beta phase being 5.29 days. The half-life of non-protein-bound CDDP was 1.6 hours. CDDP might have remained for a long time, because CDDP values were obtained 3 weeks after infusion and urinary recovery of CDDP showed low values. Its urinary recovery was 40.3% of the dose infusion in the first 24 hours and 48.0% in 96 hours. The protein-binding of CDDP was inhibited by sodium thiosulfate(STS) and renal urinary excretion was enhanced. Our data suggest that STS can be applied as a neutralizer of CDDP.